Methods, apparatuses and systems for collection of tissue sections

ABSTRACT

Methods, apparatuses and systems for facilitating automated or semi-automated collection of tissue samples cut by a microtome. In one example, a collection apparatus may be moved back and forth between respective positions at which the collection apparatus is operatively coupled to a microtome so as to collect cut tissue samples, or routine access to the microtome is provided. Relatively easy movement and positioning of the collection apparatus is facilitated, while at the same time ensuring structural stability and appropriate alignment and/or isolation between the collection apparatus and the microtome. A fluid reservoir receives samples cut by the microtome, and the collection apparatus may collect samples via a conveyor-like substrate disposed near/in the reservoir. A linear movement of the substrate may be controlled based on a cutting rate of the microtome, and the fluid level in the reservoir may be automatically maintained to facilitate effective sample collection.

RELATED APPLICATIONS

This application is a continuation claiming the benefit under 35 U.S.C.§ 120 of U.S. patent application Ser. No. 15/670,784 filed Aug. 7, 2017,entitled “Methods, Apparatuses and Systems for Collection of TissueSections,” which is a continuation claiming the benefit under 35 U.S.C.§ 120 of U.S. patent application Ser. No. 13/821,028 filed Oct. 15,2013, entitled “Methods, Apparatuses and Systems for Collection ofTissue Sections,” which is a national stage filing under 35 U.S.C. § 371of international PCT application PCT/US2011/050704 filed Sep. 7, 2011,entitled “Automatic Tape-Collection Mechanism for Ultramicrotomes,”which claims priority to U.S. Provisional Application No. 61/393,185filed Oct. 14, 2010, entitled “Methods, Apparatuses and Systems forCollection of Tissue Sections,” and to U.S. Provisional Application No.61/380,484 filed Sep. 7, 2010, entitled “Automatic Tape-CollectionMechanism for Ultramicrotomes,” the entire contents of each beingincorporated herein by reference.

GOVERNMENT FUNDING

This invention was made with government support under MH094271, NS020364and NS069407 awarded by National Institutes of Health. The U.S.government has certain rights in the invention.

DESCRIPTION OF RELATED ART

Today neuroscientists are routinely carrying out increasingly advancedphysiological experiments and cognitive scientists are proposing andtesting increasingly comprehensive models of brain function. Suchexperiments and models involve brain systems where incompleteinformation regarding the system's underlying neural circuitry presentsone of the largest barriers to research success. It is widely acceptedwithin the neuroscience community that what is needed is a comprehensiveand reliable wiring diagram of the brain that will provide aneuroanatomical scaffolding (and a set of foundational constraints) forthe rest of experimental and theoretical work in the neuro- andcognitive sciences. The current approach of attempting to integratethousands of individual in vivo tracing experiments into a coherentwhole has been considered to be a virtually impossible task.

There is an alternative approach that avoids the problem of stitchingtogether the results of thousands of in vivo tracer injectionexperiments. The imaging of a single post-mortem brain at a sufficientlyhigh resolution to resolve individual neuronal processes and synapses,while maintaining registration across size-scales, would allow directtracing of a brain's connectivity. Researchers using the raw data insuch a synapse-resolution brain connectivity atlas would be able to mapall the regions, axonal pathways, and synaptic circuits of the brain;and unlike separate specialized experiments, the results wouldimmediately and easily be integrated because they are all performed onthe same physical brain.

The creation of such a synapse-resolution atlas has been achieved fortiny invertebrate animals such as C. Elegans (a round worm measuring 1mm in length and less than 100 um in diameter). The fundamentaltechnology used, that of serial section electron reconstruction,currently requires the painstaking manual production of thousands ofextremely thin (<1 μm) tissue slices using a standard ultramicrotome inwhich newly sliced tissue sections are floated away from the cuttingknife on water and manually placed on slotted TEM specimen grids a fewsections at a time.

Because of the manual nature of this current process, this technique isimpractical to apply to larger brain structures and so it is currentlyunable to address the needs of the larger community of neuroscientistswho require a map of the brain connectivity of rodent and primatebrains. Extending these manual tissue imaging technologies to mapstructures that are 1×10⁵ (mouse brain) and 1×10⁸ (human brain) times aslarge as C Elegans presents a significant challenge.

There are a number of patents pertaining to microtomes and theirautomation. However, these designs are targeted toward automating theslicing process only, and do not address the tissue collection andhandling processes. Today the term “automated microtome” has becomesynonymous with a manual microtome merely having motorized knifeadvance. Thus, current conventional “automated microtome” designs stillrequire manual slice retrieval and manual slide or grid mounting forimaging.

A tissue sample sectioned by an ultramicrotome typically results infragile strips of tissue that come off the ultramicrotome knife andfloat on a surface of water contained within a knife boat of theultramicrotome. The fragile strips of tissue are manually collected ontoslot grids for use in transmission electron microscopy (TEM) byemploying a highly unreliable and painstaking positioning process. Theprocess involves the use, by a highly trained technician, of an“eyelash” instrument to maneuver the fragile sections onto the slotgrid(s). Such manual slice retrieval necessitates that skilled,delicate, and incredibly time-consuming work be expended on each tissueslice (or small series of slices) as it involves “fishing” each tissueslice out of a water boat attached to the knife of the conventionalultramicrotome instrument and onto a TEM grid. Such a collection processdrastically limits the total volume of tissue that can be sectioned andimaged. In addition, no matter how experienced and skilled thetechnician may be at moving tissue strips to the slot grids, manualintervention will inevitably result in damage to at least some of thecollected tissue sections. Further, the manual nature of the collectingprocess also requires continual starting and stopping of theultramicrotome to allow for the tissue sections to be manuallycollected, adversely impacting the precision of the cutting process. Tocompensate for such disturbances, tissue sections are typically cutthicker, thus, limiting the overall resolution of electron microscopyimaging to be performed on the tissue.

SUMMARY

The inventors have recognized and appreciated that automating in somemanner a tissue sample collection process (e.g., in connection withslicing thin tissue samples using a conventional ultramicrotome) wouldmitigate potential damage to samples collected during a manualcollection process, and significantly facilitate imaging of greaternumbers of collected samples. In these respects, automated tissue samplecollection techniques would provide an appreciable advance towardmapping larger tissue structures.

In view of the foregoing, various inventive embodiments disclosed hereinrelate generally to apparatus, systems and methods for facilitatingautomated collection of tissue samples that are sliced from a microtome.In one exemplary implementation, a collection apparatus that is placedinto coupling engagement with a microtome such that the collectionapparatus collects thin tissue sections sliced from the microtome. Thecollection apparatus may be adapted to move back and forth repeatedlyfrom a position that is suitable for automated and prolonged collectionof thin tissue sections. When the collection apparatus is not in anappropriate position for automated and prolonged thin tissue sectionretrieval, thin tissue sections may be collected from the microtomeaccording to routine methods (e.g., the eyelash method).

Systems and methods described also relate to automatically maintainingfluid contained in a reservoir of the microtome at a level suitable forautomated and prolonged collection of thin tissue sections. In somecases, a current level of fluid within the reservoir is monitored withrespect to an edge of a microtome-quality knife. When the current levelof fluid within the reservoir drops below an operating level suitablefor automated and prolonged thin tissue section collection, fluid isautomatically introduced into the reservoir to restore the current levelof fluid within the reservoir to the suitable operating level. Acomputing device having a processor may be subject to feedback controland used in conjunction with a fluid input apparatus to appropriatelymaintain fluid levels in the reservoir to be suitable for automatic andprolonged retrieval of thin tissue sections, for example, on to asupport substrate.

During operation of the collection apparatus to retrieve thin tissuesections from the microtome, a computing device having a processor maybe used in conjunction with appropriate monitoring equipment, to monitorthe rate at which a tissue sample is sliced by the microtome knife.According to the rate at which thin tissue sections are produced, thespeed of a support substrate moving along the collection apparatus maybe controlled for appropriate collection of thin tissue sections on tothe support substrate.

In an illustrative embodiment, a device for processing a tissue sampleis provided. The device includes a collection apparatus for collectingat least one thin tissue section provided from a microtome, wherein thecollection apparatus is constructed and arranged to move back and forthin a repeated motion between a collecting position and a non-collectingposition relative to the microtome.

In another illustrative embodiment, a system for processing a tissuesample is provided. The system includes a microtome adapted to slice atleast one thin tissue section from a tissue sample; and a collectionapparatus for collecting the at least one thin tissue section from themicrotome, wherein the collection apparatus is constructed and arrangedto move back and forth repeatedly between a collecting position and anon-collecting position relative to the microtome.

In a different illustrative embodiment, a method for processing a tissuesample is provided. The method includes causing movement of a collectionapparatus from a non-collecting position to a collecting positionrelative to a microtome; operating the collection apparatus to collectat least one thin tissue section produced from the microtome; andcausing movement of the collection apparatus from the collectingposition to the non-collecting position relative to the microtome.

In yet another illustrative embodiment, a system for processing a tissuesample is provided. The system includes a microtome having a reservoircontaining fluid automatically maintained at a substantially constantlevel within the reservoir, the microtome adapted to slice at least onethin tissue section from a tissue sample such that the at least one thintissue section contacts the fluid within the reservoir; and a collectionapparatus for collecting the at least one thin tissue section from thefluid within the reservoir.

In a further illustrative embodiment, a method for using a microtomeincluding slicing a tissue sample with a microtome-quality knife toproduce at least one thin tissue section, and bringing the at least onethin tissue section into contact with a fluid within the reservoir ofthe microtome. The method includes monitoring a current level of fluidwithin the reservoir with respect to an edge of the microtome-qualityknife; and automatically restoring the current level of fluid within thereservoir to an operating level of fluid when the current level of fluidwithin the reservoir is less than the operating level of fluid.

In another illustrative embodiment, a non-transitory computer-readablestorage medium having computer-executable instructions adapted toperform, when executed, steps for controlling hardware coupled to thecomputer-readable storage medium for processing a tissue sample. Thesteps include monitoring a rate of slicing of the tissue sample with amicrotome-quality knife in producing a plurality of thin tissuesections; and controlling a speed of a support substrate moving on acollection apparatus in accordance with the rate of slicing of thetissue sample to collect the plurality of thin tissue sections on to thesupport substrate.

In a different illustrative embodiment, a non-transitorycomputer-readable storage medium having computer-executable instructionsadapted to perform, when executed, steps for controlling hardwarecoupled to the computer-readable storage medium for maintaining a levelof fluid in a reservoir. The steps include monitoring a current level offluid within the reservoir with respect to an edge of themicrotome-quality knife; and automatically restoring the current levelof fluid within the reservoir to an operating level of fluid when thecurrent level of fluid within the reservoir is less than the operatinglevel of fluid.

The foregoing is a non-limiting summary of the invention, which isdefined by the attached claims. Other aspects, embodiments, featureswill become apparent from the following description.

It should be appreciated that all combinations of the foregoing conceptsand additional concepts discussed in greater detail below (provided suchconcepts are not mutually inconsistent) are contemplated as being partof the inventive subject matter disclosed herein. In particular, allcombinations of claimed subject matter appearing at the end of thisdisclosure are contemplated as being part of the inventive subjectmatter disclosed herein. It should also be appreciated that terminologyexplicitly employed herein that also may appear in any disclosureincorporated by reference should be accorded a meaning most consistentwith the particular concepts disclosed herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings are not intended to be drawn to scale. In thedrawings, each identical or nearly identical component that isillustrated in various figures is represented by a like descriptor. Forpurposes of clarity, not every component may be labeled in everydrawing.

The advantages and features of this invention will be more clearlyappreciated from the following detailed description, when taken inconjunction with the accompanying drawings.

FIG. 1A is a perspective view of a tape-collecting mechanism andcylindrical tissue block;

FIG. 1B is a close-up view of the back of the tissue block of FIG. 1A,including blockface applicator mechanisms;

FIG. 1C is a close-up view of the side of the tissue block of FIG. 1Aduring operation of an automatic taping lathe-microtome;

FIG. 2A is a perspective view of a composite tape sandwich, where eachlayer in the composite sandwich is peeled away and labeled;

FIG. 2B is a view of a final composite tape sandwich from the underside;

FIG. 3A is a perspective view showing an electron tomography tapecassette with side panels removed to reveal tissue tape reels disposedwithin;

FIG. 3B is a close-up view of a specimen stage tip of the electrontomography tape cassette of FIG. 3A;

FIG. 3C is a close-up view of the specimen stage tip of the electrontomography tape cassette of FIG. 3A where the sides of the tip have beenremoved to reveal the tape path and clamping mechanism within;

FIG. 4A is a perspective view of an electron tomography tape cassettewith arrows drawn to display the main degrees of freedom of movementallowed by the mechanism;

FIG. 4B depicts a stylized transmission electron microscope (TEM) withthe electron tomography tape cassette of FIG. 4A inserted into itsspecimen port;

FIGS. 4C, 4D, and 4E are three close-up views of the electron tomographytape cassette of FIG. 4A detailing how the entire cassette mechanism canrotate relative to the TEM in order to perform a tomographic tilt-serieson the tissue sample at the tip;

FIG. 5A is a schematic side view of an embodiment;

FIG. 5B is a schematic side view of another embodiment;

FIG. 5C is a schematic side view of a further embodiment;

FIG. 5D is a schematic side view of yet another embodiment;

FIG. 5E is a schematic side view of a different embodiment;

FIG. 6A is a front plan view of a nanosectioning lathe ultramicrotomeaccording to an embodiment of the present invention;

FIG. 6B is a perspective view of a nanosectioning lathe ultramicrotomeaccording to an embodiment of the present invention;

FIG. 7 is a close up perspective view of a knife stage, tissue axle, andconveyor belt collection mechanism according to an embodiment of thepresent invention;

FIG. 8A is a side plan view of a nanosectioning lathe ultramicrotomewithout some sensors according to an embodiment of the presentinvention;

FIG. 8B is a side plan view of a nanosectioning lathe ultramicrotomewith a sensor and PID feedback mechanism according to an embodiment ofthe present invention;

FIG. 9A is a side plan view of a nanosectioning lathe ultramicrotomewith a conveyor belt mechanism according to an embodiment of the presentinvention;

FIG. 9B is a side plan view of a nanosectioning lathe ultramicrotomewith a conveyor belt mechanism in operation according to an embodimentof the present invention;

FIG. 10A is a side plan view of a nanosectioning lathe ultramicrotomewith a conveyor belt mechanism in operation where the thin tissuesection is continuously sliced according to an embodiment of the presentinvention;

FIG. 10B is a side plan view of a nanosectioning lathe ultramicrotomewith a conveyor belt mechanism in operation where the thin tissuesection length is longer than the distance from the knife edge to theconveyor belt according to an embodiment of the present invention;

FIG. 10C is a side plan view of a nanosectioning lathe ultramicrotomewith a conveyor belt mechanism in operation where the thin tissuesection length is shorter than the distance from the knife edge to theconveyor belt according to an embodiment of the present invention;

FIG. 11A is a perspective view of a system for processing tissue samplesin accordance with embodiments described;

FIG. 11B is a close up perspective view of the collection apparatus ofFIG. 11A;

FIG. 11C is another close up perspective view of the collectionapparatus of FIG. 11A;

FIG. 12 is a perspective view of portions of a system for processingtissue samples in accordance with embodiments described;

FIG. 13A is a perspective view of the system of FIG. 11A where acollection apparatus is moved away from a microtome;

FIG. 13B is a perspective view of the system of FIG. 13A where thecollection apparatus is moved further away from the microtome;

FIG. 14A is a close up perspective view of a conveyor portion and afluid reservoir of a microtome in accordance with embodiments described;

FIG. 14B is a close up perspective view of the conveyor portion andfluid reservoir of FIG. 14A with fluid disposed in the reservoir inaccordance with embodiments described;

FIG. 15A is a screenshot of a user interface in accordance withembodiments described.

FIG. 15B is a view of a fluid input apparatus in accordance withembodiments described.

FIG. 15C is a close up view of a fluid input apparatus engaged with areservoir in accordance with embodiments described.

FIG. 16A is a side plan view of a collection apparatus in accordancewith embodiments described;

FIG. 16B is a perspective view of the collection apparatus of FIG. 16Ain accordance with embodiments described;

FIG. 16C is a side plan view of the collection apparatus of FIG. 16A incoupled arrangement with a microtome in accordance with embodimentsdescribed;

FIG. 17 is a perspective view of a conveyor portion of a collectionapparatus in accordance with embodiments described;

FIG. 18 is a perspective view of adjustment features of a collectionapparatus in accordance with embodiments described;

FIG. 19 is another perspective view of adjustment features of acollection apparatus in accordance with embodiments described; and

FIG. 20 is a perspective view of an enclosure for a system forprocessing tissue samples in accordance with embodiments described.

DETAILED DESCRIPTION

It should be understood that aspects of the invention are describedherein with reference to the figures, which show illustrativeembodiments in accordance with aspects of the invention. Theillustrative embodiments described herein are not necessarily intendedto show all aspects of the invention, but rather are used to describe afew illustrative embodiments. Thus, aspects of the invention are notintended to be construed narrowly in view of the illustrativeembodiments. It should be appreciated, then, that the various conceptsand embodiments introduced above and those discussed in greater detailbelow may be implemented in any of numerous ways, as the disclosedconcepts and embodiments are not limited to any particular manner ofimplementation. In addition, it should be understood that aspects of theinvention may be used alone or in any suitable combination with otheraspects of the invention.

I. OVERVIEW

Various embodiments disclosed herein relate generally to automatedcollection of tissue samples (also referred to herein as “thin tissuesections”) cut from a microtome. In some exemplary implementations,collection apparatuses and associated methods may be employed withvarious types of conventional microtomes, wherein the microtome isunmodified and the collection apparatuses and methods are configured asan add-on or retrofit to be used in conjunction with the microtome tofacilitate automated tissue sample collection. In other implementations,some modifications may be made to a conventional microtome to facilitateintegration with automated sample collection apparatuses and methodsaccording to the inventive concepts described herein. In yet otherimplementations, an integrated system is contemplated including amicrotome comprising various inventive features disclosed hereinrelating to automated sample collection features, and/or a microtome(either conventional or modified) that is operatively coupled to anautomated sample collection apparatus.

For example, in some embodiments, collection apparatuses may bepositioned in a coupled arrangement with any appropriate microtome wherethin tissue sections cut from the microtome can be automaticallycollected on to a support substrate for long periods of time and withoutadded user intervention. When not positioned in a coupled arrangementwith a microtome in a manner that supports automatic retrieval of thintissue sections for long time periods, collection apparatuses describedmay be disposed in a position apart from the microtome so as not tointerfere with the ability for a user to perform standard microtomeactivities (e.g., performing block trimming, setting the position of theknife, initial microtome sectioning, eyelash method collection of tissuesections, etc.).

In the foregoing embodiment, when automatic and prolonged collection oftissue sections from the microtome is desired, the collection apparatusmay be moved toward and into coupled engagement with the microtome. Inexemplary implementations, the collection apparatus may be constructedand arranged to facilitate relatively easy movement and positioning ofthe collection apparatus by a user (e.g., technician/operator) into andout of coupled engagement with a microtome, while at the same timeensuring structural stability and appropriate alignment and/or isolationof the collection apparatus. In other implementations, movement andpositioning of the collection apparatus into and out of coupledengagement with a microtome may be accomplished automatically orsemi-automatically (e.g., without significant user intervention).

In one aspect, when a collection apparatus is disposed in a suitablecollecting position, thin tissue sections produced from the microtomemay be automatically collected on to a suitable support substratewithout user intervention. In some cases, even when the collectionapparatus is coupled with the microtome in a collecting position, amicrotome user may still have access to certain functions of themicrotome (e.g., usage of control panel, hand wheel, stereo microscope,water boat access, etc.).

For instances when manual collection of tissue sections is desired, thecollection apparatus may be appropriately moved away from and out ofengagement with the microtome, providing space for the operator toperform manual collection. Accordingly, a collection apparatus may becaused to move back and forth repeatedly between a collecting positionand a non-collecting position relative to the microtome. Such movementbetween collecting and non-collecting positions may be effected manuallythrough user intervention, or alternatively, movement of the collectionapparatus may occur automatically through actuation via a controldevice.

It should be appreciated that collection apparatuses described are notlimited to the type of microtome the collection apparatus may be placedin coupled arrangement with, and may be suitable for use with anyappropriate microtome. For example, collection apparatuses described maybe appropriately coupled to any microtome known in the art, such as andwithout limitation, rotary microtomes, lathe microtomes,ultramicrotomes, sled microtomes, vibrating microtomes and lasermicrotomes. Although aspects of the invention are not so limited,embodiments of collection apparatuses coupled with lathe microtomes andultramicrotomes are described in further detail below.

Apparatuses, systems and methods described herein also may provide forfluid contained in a reservoir of a microtome to be automaticallymaintained at a level suitable for producing thin tissue sections and tosupport automated collection of the thin tissue sections in a reliableand prolonged manner. For example, during automated collection, thecurrent level of fluid within the reservoir may be monitored and adetermination made as to whether the current level of fluid is within anoperating level suitable for reliably slicing a tissue sample to produceand continuously collect thin tissue sections on to a support substrate.In an embodiment, if the current level of fluid is below a threshold ofthe operating level required for automatic and continuous operation ofthe collection apparatus for prolonged periods of time (e.g., more than30 minutes), then additional fluid is automatically introduced into thereservoir (e.g., via a fluid input apparatus coupled to the reservoir)for restoring the current fluid level to a suitable operating level.

Aspects of a microtome and/or collection apparatus may be controlledthrough executable instructions suitably encoded on to a computingdevice electrically coupled to the microtome and/or the collectionapparatus. In certain embodiments, appropriate software instructions areencoded on to a computing device coupled to the microtome throughappropriate hardware so as to control the level of fluid within thereservoir of the microtome to be appropriately maintained for continuousand automatic operation of the microtome and collection of thin tissuesections. Automated collection of thin tissue sections may occur forprolonged periods of time (e.g., more than 30 minutes, more than 12hours, several days, etc.).

In some embodiments, appropriate executable instructions are encoded onto a computing device in a system coupled with a microtome and acollection apparatus for monitoring a rate at which a tissue sample issliced to produce thin tissue sections. Based on the rate of thin tissuesection production, the system controls the speed of movement of thesupport substrate on the collection apparatus to match the rate ofsectioning so as to automatically collect thin tissue sections in anorderly fashion. In certain embodiments, executable instructions encodedon to a computing device in a system coupled to a collection apparatusprovide for monitoring of the tension of a support substrate on thecollection apparatus and controlling the tension of the supportsubstrate so as to automatically and continuously collect thin tissuesections in a suitable manner.

The collection apparatus may have a conveyor portion at least partiallysubmerged in fluid contained within a reservoir and in close proximityto the edge of a microtome knife. Tissue sections that slide off asurface of the knife float on the surface of the fluid and are retrievedby a moving support substrate on the conveyor portion. In oneembodiment, the support substrate is controlled so as to move at a speedmatching the speed of microtome slicing so that each section is gentlypulled off the fluid surface and laid flat on to the substrate surface,without bunching or layering together of the tissue sections. In someembodiments, automatic collection is permitted without user interventionfor more than twelve hours, thereby facilitating collection of thousandsof sections between 10 and 50 nm thick (e.g., approximately 30 nmthick).

Systems that involve methods for automatic collection of thin tissuesections produced from a microtome are disclosed in U.S. PatentPublication No. 2010/0093022 entitled “Methods and Apparatuses forProviding and Processing Sliced Thin Tissue”; U.S. Pat. No. 7,677,289entitled “Methods and Apparatuses for the Automated Production,Collection, Handling, and Imaging of Large Numbers of Serial TissueSections”; and U.S. Provisional Application No. 60/867,487, filed Nov.28, 2006, entitled “Methods and Apparatus for Providing and ProcessingSerial Tissue Sections” all of which are incorporated herein byreference in their entirety. Accordingly, a large volume of thin tissuesections may be automatically collected on to a support substrate andimaged at nanometer resolution, for example, by electron microscopy suchas TEM and/or scanning electron microscopy (SEM). Following below is adescription of exemplary systems according to the above-identifiedreferences to provide appropriate context for collection apparatuses andmethods, and integrated systems of collection apparatuses andmicrotomes, described in greater detail herein.

II. EXEMPLARY METHODS, APPARATUSES AND SYSTEMS BASED ON INTEGRATEDSYSTEMS

The above-identified references relate generally to an automatic tapecollecting lathe ultramicrotome (ATLUM), in which the basic cuttingmotion of the microtome is redesigned, replacing the conventionaldiscontinuous ratcheting motion with a continuous rotary motion of alathe. In other aspects, irrespective of cutting based on lathe-likecontinuous rotary motion or discontinuous ratcheting motion, otheraspects of the above-identified references relate to the production oftissue samples and appropriate mounting of samples on substrates tofacilitate various imaging techniques involving electron microscopy and,in particular, scanning electron microscopy (SEM). It should beappreciated that automated collection apparatuses, systems and methodsdescribed in greater detail below may be based on or incorporate severalconcepts relating to an ATLUM and/or production of tissue samplessuitable for imaging based on electron microscopy; at the same time, itshould be understood that collection apparatuses, systems and methodsdescribed herein are not limited to application with an ATLUM orparticular techniques for preparing collected samples for imaging.

In an ATLUM, a block of tissue sample having various geometries may besliced into a continuous ribbon of thin tissue, or multiple thin tissuesections, and disposed on an appropriate substrate to facilitatesubsequent imaging of the sliced thin tissue. A continuous lathe cuttingdesign may provide for continuous taping and slice collection. Amechanically stable, reliable, fast, and easily constructed design mayresult, facilitating fully automated production, collection, handling,imaging, and storage of thousands of semi-thin and ultra-thin tissuesections.

Closed-loop control of section thickness of thin tissue sections orribbons sliced from a tissue sample may be implemented to producethinner sliced tissue sections or ribbons having tightly controlledthickness. Thinner samples with predictable thickness in turn facilitatehigh quality volume reconstructions of biological samples. In oneexemplary implementation, one or more capacitive sensors are employed inan ATLUM to facilitate regulation of a distance between a slicing knifeand a tissue sample to be sliced, thereby controlling sliced tissuethickness with improved precision. Other types of distance sensingtechniques may be employed in other implementations to control andregulate sliced tissue thickness.

Thin tissue sections or ribbons may be particularly processed/preparedto facilitate imaging with a scanning electron microscope (SEM) (e.g.,in electron backscatter mode). Imaging via a SEM is generally asignificantly simplified process as compared to imaging via a TEM(transmission electron microscope), and images may be obtained via SEMof sufficient quality, and in many instances equivalent quality, toconventional TEM images. Collected tapes of thin tissue sections orribbons sliced from a tissue sample are used to create UltraThin SectionLibraries (UTSLs) that allow for fully automated, time-efficient imagingin the SEM.

Accordingly, thinner tissue sections having tightly controlled thicknessmay be produced in a fully automated fashion. In exemplary applications,tens of meters of ultrathin sections may be automatically sliced andcollected on a tape that is subsequently stained with heavy metals andmounted onto plates for any appropriate imaging mode in a scanningelectron microscope (SEM), such as, but not limited to, electronbackscatter imaging. Sections retrieved by automated collection systemsdescribed herein may provide images equivalent to TEM images, showingdetail down to individual synaptic vesicles within synapses. Automatedcollection systems can also quickly create a UTSL of many cubicmillimeters of tissue, enough to encompass multiple brain regions andtheir interconnecting axonal tracts. The UTSL can also be swiftly SEMimaged, and this can be used to intelligently direct subsequent timeintensive high-resolution imaging forays. In this manner, researchersmay efficiently map out specific neural circuits spanning severalmillimeters with a resolution in the nanometer range.

A general discussion of suitable methods for collecting thin tissuesections cut from a microtome will now be provided in accordance with anumber of illustrative examples. FIG. 1A is a perspective view detailingthe tape-web mechanism 300 and cylindrical tissue block 160 only. Thelathe body and cross-slide components have been removed for clarity.FIG. 1B shows the same mechanism, but a close-up view from behind thetissue block detailing the blockface application mechanism. FIG. 1C is aclose-up view of the side of the tissue block during operation.

Starting at the top of the mechanism, a top base tape feed roll 304supplies a continuous stream of plastic tape 305 into the mechanism. Atape hole puncher mechanism 306 punches square viewing holes into theplastic top base tape 305. The tape is driven forward by tape driverollers 308 which maintain a slack (no tension) region 309 in the web.This slack region assures that no tension forces from the tape disturbthe motion of the cylindrical tissue block 160 or the blockface tapingprocess.

The slack, hole-cut tape 309 is adhered to the block 160's surface at ablockface taping pressure roller 330. The timing of the hole cuttingperformed by the tape hole puncher mechanism 306 is synchronized to thecurrent angle of the cylindrical tissue block 160 such that each holewill be precisely aligned directly over an embedded tissue cube 140 whenthe tape 309 is adhered to the block 160. A section 332 of top base tapeis adhered for a quarter-turn of the block 160 before it is sliced offthe block 160 at the knife 214 along with a thin ribbon 402 (detailed inFIG. 2A) of the tissue block 160. The thickness of this ribbon of tissueis set by the relative rotary speed of the lathe spindle 206 and thelinear speed of the knife 214. Both speeds are constant and serve to cutoff a continuous spiral ribbon of embedded tissue 402 which is alreadyadhered to the tape 332 at the time of cutting producing a freshlymicrotomed ribbon of tissue adhered to top base tape 334.

The ribbon of tissue adhered to tape 334 is reeled up by a finalcomposite tissue tape-sandwich take-up reel 302, but before it getsthere the tape 334 is driven past a bottom base tape applicator (andblowout hole mechanism) 336 that applies (prints) a covering bottom basetape 410 (detailed in FIG. 2A). The blowout hole function of 336 will bediscussed later during the section on tape imaging. This produces aTEM-ready composite tape sandwich (abbreviated tissue-tape) 338 which isreeled up onto take-up reel 302.

FIGS. 1B and 1C more clearly show the blockface preparation stepsleading up to the production of the adhered section of tape 332. Thefreshly cut surface of cylindrical tissue block 310 comes into contactwith the TEM support film head 312 which lays down a thin-film on theentire surface of the block with the help of a smoothing and dryingroller mechanism 314. This produces a support film coated block surface316. This surface next comes in contact with two adhesive stripapplicator heads 318 that, with the help of a smoothing and dryingroller mechanism 320, lay down two strips of adhesive on the block face322. This section of the block's surface with TEM support film andadhesive strips applied is now ready to accept the hole-cut tape 309 forblockface taping via the pressure roller 330.

FIG. 2A shows the composition of the tissue-tape 338. FIG. 2B shows thebackside of the tissue-tape. In these figures, each layer in thecomposite sandwich has been peeled away and labeled. The tissue tape 338includes a composite tape-sandwich where the microtomed ribbon cut offthe tissue block 402 is secured and protected between top 408 and bottom410 base tapes. A multitude of 1 mm² microtomed tissue slices 400 (each100 nm to 1 μm thick) are seen to be embedded in the ribbon 402.Further, this ribbon 402 is covered by a TEM support film coating 404providing support for each tissue slice 400 across the viewing slots(holes) in tapes 408 and 410 (these holes are labeled 409 in the toptape FIG. 2A, and 411 in the bottom tape FIG. 2B). The adhesive strips406 laid down by the applicator heads 318 just before blockface tapingby pressure roller 330 are seen clearly in FIG. 2A. Notice how thesestrips avoid obstructing the view of the tissue slices 400 but stillprovide adherence between the tissue ribbon 402 and the top tape 408.

Seen in the close up view offered by FIG. 2A, one can appreciate thetissue-tape 338's similarity to the film in a movie projector. Eachtissue slice 400 resides in its own frame, acting as a TEM slot grid.This analogy to the film in a movie projector can be taken further. Inthis form, the tissue-tape 338 can be reeled up without damage to thedelicate tissue slices 400 since the slices are protected on both sidesby the base tapes 408 and 410. These reels of tissue-tape can be handledand stored efficiently, and can be fed into an electron tomography tapecassette 500 (shown in FIG. 3A) for fast random access ultrastructureimaging in a standard commercial TEM.

FIG. 3A shows the electron tomography tape cassette 500. Side panelshave been removed to reveal two tissue-tape reels 506. The electrontomography tape cassette 500 is designed to act like a standard TEMspecimen stage, and thus can slide into the specimen port of a standardTEM 530 (see FIG. 4B). The main difference between the electrontomography tape cassette and a traditional TEM specimen stage is theaddition of a set of tape reels and motors 506 for mounting the tissuetape 338 on, and the addition of internal mechanisms that allow thetissue tape 338 to be fed all the way out to the specimen stage's tip508 and thus into the TEM's electron beam for ultrastructure imaging ofthe tissue slice 510 clamped at the stage's tip 508. There is a TEMmounting flange 502 which secures the body of the electron tomographytape cassette 500 to the side of a TEM 530. There is also a cylindricalspecimen stage body 504 which slips into the vacuum port on the TEM 530and forms a tight vacuum seal with it, yet simultaneously allowsrotation around the long axis of the cylindrical specimen stage body504. This rotation allows the incidence angle at which the electron beamimpinges upon the tissue slice 510 to be varied by rotating the entireassembly of the cylindrical specimen stage body 504 and the cassettereels and motors 506 relative to the mounting flange 502 (see FIGS. 4C,4D, and 4E). This rotation of the cylindrical specimen stage body 504relative to the flange 502 is driven by a drive motor 512. Changing thisangle of incidence allows for 3D reconstruction of the tissue slicehaving better resolution in depth than the slice thickness would allowif only 2D (non-tilt series) imaging were performed, and is a standardtechnique in electron microscopy today.

FIG. 3B shows a close-up view of the specimen stage tip 508. FIG. 3C isa close-up view of the specimen stage tip 508 where the sides of the tiphave been removed to reveal the tape path and clamping mechanism within.The tissue-tape 338 wraps around a pulley 524 at the very front of thetip 508. During operation, the tape drive motors 506 reel the tissuetape 338 such that the tissue slice to be imaged 510 is centered betweentwo top clamps 520 and is thus inline with the TEM's electron beam.These two top clamps 520 then engage, securing that section oftissue-tape containing the slice to be imaged 510 stably in position.The pulley 524's position is then adjusted electronically to lengthen orshorten the section of tape 338 between the top clamps 520 and a pair ofbottom clamps 521 in order to bring a blowout hole 522 into positionbetween the two bottom clamps 521. These bottom clamps 521 are thenengaged to secure the entire tape 338 for imaging.

This blowout hole 522 is one of a multitude of blowout holes spacedperiodically throughout the tape 338. These holes are made within theautomatic taping lathe microtome's bottom tape applicator and blowouthole mechanism 336 by simply directing a puff of air at the fragilesection of sliced ribbon 402 in periodically spaced frames of the tissuetape 338. Recall that a few tooth-indentation cavities 132 arespecifically left empty of tissue cubes 140 during the embedding processfor this reason. Thus, the final axle-mounted tissue block 160 had threetissue-free regions 162 around its periphery. These holes 522 arepurposely blown out to allow the wrapped around section of the tissuetape 338 which resides between the bottom clamps 521 to not obstruct theimaging of the tissue slice 510 directly above it. The cutaway view ofthe specimen stage tip 508 in FIG. 3C shows both sets of clamps 520 and521 engaged securely holding a single slice of tissue 510 in positioninline with the TEM's electron beam. Directly below this tissue slice510 is a blowout hole 522 in the tissue tape 338 and thus only theparticular slice to be imaged 510 will be seen by the TEM's electronbeam.

FIG. 4A shows the electron tomography tape cassette 500 with arrowsdrawn to display the main degrees of freedom of movement allowed by themechanism. The reels of tissue tape 506 can rotate in synchrony to bringany desired slice of tissue in the tape out to the specimen tip and thusinto the electron beam for imaging. Exact positioning of the field ofview is set by driving the whole tip mechanism along the two degrees offreedom perpendicular to the electron beam's cavity (depicted by arrowsshown near tip). Also, the entire cassette and stage body 504 can rotaterelative to the TEM mounting flange 502 as described below.

FIG. 4B depicts a stylized transmission electron microscope (TEM) withthe electron tomography tape cassette inserted into its specimen port.The tape cassette (with cassette covers, which were removed in previousview, installed) is hermetically sealed and can thus share the TEM'svacuum via its seal along the stage's body 504. The tissue tape 338within the tape cassette 500 is electronically advanced using reelmotors 506 to bring a particular tissue slice 510 to be imaged inlinewith the TEM's electron beam. Clamps (520 and 521) engage to allowstable unobstructed viewing of the slice 510. Any X-Y motions of thestage are now performed to address a small section within the slice(using standard X-Y specimen stage motors present in the electrontomography tape cassette 500 but, for clarity, not depicted here). Atomographic tilt-series (a set of 121 2D electron micrograph images ofthe tissue slice 510) can be taken by stepping the incidence angle in 1°increments from −60° to +60°.

In FIGS. 4C, 4D, and 4E the manner in which the body of the electrontomography tape cassette rotates relative to the TEM mounting flange 502is depicted. Those three figures show the tape cassette mechanism atthree different incidence angles (−60°, 0°, and +60° respectively).

At each angle, a 2D electron micrograph is produced and all 121 of theseimages are fed into a standard electron tomographic volumereconstruction algorithm in order to compute a 3D voxel volume digitalimage of the particular piece of tissue 510 under examination. Thesystem is designed such that any of the multitude of tissue slices inthe tissue-tape 338 loaded into the electron tomography tape cassette500 can be randomly and automatically accessed for 2D or 3D tomographicimaging (at ultrastructure resolution) without ever cracking the vacuumof the TEM. Thus, this avoids any time-consuming manual intervention inthe imaging process.

The following describes some alternative examples for the automatictaping lathe-microtome. The following descriptions of alternativeexamples of the invention are presented for the purposes of illustrationand description. They are not intended to be exhaustive or to limit theinvention to the precise form disclosed. Some of these alternativedesigns involve variations on the blockface taping and tissue collectionprocesses, as depicted in a series of schematic side views in FIGS. 5Athrough 5D. The previously disclosed example is re-represented in FIG.5E in this same schematic form to further promote ease of comparison.

FIG. 5A shows a minimalist core design (alternative design #1) of thelathe-microtome. The axle-mounted cylindrical tissue block 160 isrotated against the knife 214 in order to liberate a thin ribbon oftissue slices in embedding medium 402. There is no blockface taping inthis design (just thin-film support film deposition by 312 and 314) andso a boat 600 filled with water 602 must be attached to the knife 214 inorder to collect the fragile un-taped tissue ribbon 402 as it comes offthe knife. In this design, once the tissue ribbon becomes longer thanthe water boat, manual collection of the tissue ribbon is required, thusthis design cannot be considered truly automated.

FIG. 5B show alternative design #2. This is a modification to theminimalist core design in which a submerged conveyor belt 610 is made upof the bottom base tape 410 looped around a pulley 612 firmly attachedto the knife's water boat and submerged in its water 602. Thisarrangement allows the fragile floating tissue ribbon 402 to be gentlyand continuously lifted out of the water by the conveyor belt 610 asshown in the figure. A bottom base tape hole punching mechanism 614punches viewing holes in the bottom base tape, and its punches aresynchronized with the angle of the tissue block 160 such that eachtissue slice 400 in the tissue ribbon 402 resides over a viewing hole.The top tape 408 after having similar viewing holes punched in it byhole puncher 306 is aligned and pressed onto the top of the conveyorbelt by pressure roller 616. This produces a tape-sandwich which can besealed by a sealing mechanism (e.g. a heated pressure roller) 618 beforefinally being reeled up as a finished TEM-ready tissue tape. This designis fully automated and produces a tissue tape-sandwich capable ofautomated imaging using the electron tomography tape cassette 500. Thisdesign (FIG. 5B) does not employ blockface taping meaning that there isa place in the mechanism where a fragile, freely-floating ribbon oftissue 402 is unsecured by any base tape. This reduces the reliabilityof the design, but it also reduces its complexity by eliminatingblockface taping.

FIG. 5C shows alternative design #3 which simply adds blockface tapingto the submerged conveyor-belt design. This design is similar to thepreviously disclosed embodiment's in its use of a blockface tapingpressure roller 330 adhering the top base tape 408 directly to theblockface before cutting. In this way there is never a fragile,unsupported tissue ribbon. This design has both the advantage ofblockface taping tissue support at the knife and the advantage of aknife water boat to prevent friction-induced damage with the knife. It,however, suffers from the complexity of both a water boat and blockfacetaping mechanism.

FIG. 5D shows alternative design #4 in which the water boat has beenremoved and the conveyor-belt formed by the bottom base tape is nolonger submerged. The blockface taping has provided enough support forthe tissue ribbon 402 coming off the knife 214 such that the water boatsupport can be eliminated.

Finally, FIG. 5E shows the previously disclosed example in the sameschematic manner as the just described alternative designs. In it, theconveyor-belt made up of the bottom tape is replaced by a printing head336 that manufactures the bottom base tape 410 in situ. This simplifyingchange can be tolerated if the final tissue tape-sandwich still hassufficient strength provided now only by the top tape. The in situmanufactured bottom tape is then only acting as a relief to protect thetissue from friction damage during reel-up operations.

Another alternative example, which is not depicted in the figures, is toforgo cutting viewing holes in the top and/or bottom base tapes withinthe microtome, and instead, as a later step, etch these holes using anacid to reveal the tissue slices within. If the top and bottom basetapes are made of a solid material (preferably a metal such as copper)and no holes are cut in the microtome in these tapes, then the compositetape sandwich taken-up on the final take-up reel 302 will not be readyfor imaging since the tissue slices between the top and bottom tapeswill be hidden by the overlying tapes. This tape-sandwich can then beput through an etching machine where a mask is placed around eachsection of tape covering up all areas of tape except those having tissuedirectly beneath. Then the tape is exposed to an etchant (acid in thecase of metal tapes) that will dissolve the parts of the top and bottomtape directly above and below each tissue slice. The etchant is chosenso as not to damage the delicate tissue slice which is revealed via theetching process. The advantage of this viewing hole etching method isthat it allows the blockface taping step to proceed with a solid tapeinstead of one with viewing holes. This implies that the tissue slicebeing cut can be supported across its entire width during the cuttingprocedure.

Yet another example of the present invention is directed to theproduction and preparation of “tissue tapes” (one or more thin tissuesections or ribbons disposed on a substrate) that may be imaged with ascanning electron microscope (SEM). As discussed above, various examplesof lathe microtomes may be designed to produce tapes for transmissionelectron microscope (TEM) imaging; however, according to other examples,images may be maintained via an SEM, generally resulting in asignificant simplification of the overall process, while obtaining SEMimages of sufficient (e.g., equivalent) quality to standard TEM images.In one aspect of this example, tissue tapes prepared and collected viaan ATLUM may be used to create UltraThin Section Libraries (UTSLs) thatallow for fully automated, time-efficient imaging in the SEM.

In one exemplary TEM implementation described above, the block face wascoated continuously with a TEM support film and a metal tape was used tocollect the cut sections. This metal tape was later etched with holes toreveal the tissue sections and make them ready for transmission EMimaging. In some instances this may be a complicated process and as suchmay reduce reliability. In contrast to TEM imaging, in examples directedto producing tissue tapes ready for SEM imaging, the automatic lathemicrotome process may be improved in one or more of the following ways:SEM imaging eliminates the need to create viewing holes in the tissuetape (either during the collection process or after the tape iscollected); SEM imaging eliminates the need for TEM support film; SEMimaging allows use of a (carbon coated) plastic collection tape such asboPET (biaxially-oriented polyethylene terephthalate) as opposed tometal tape (plastic tapes do not wrinkle, are more dimensionally stable,and are in general better suited to the automatic tape collectionmechanism of the lathe microtome); SEM imaging allows the entire tissuetape to be imaged (TEM viewing holes left some parts of the tapeobscured), which allows for much larger regions of tissue to be imaged;the resulting tissue tapes for SEM imaging are more robust to handlingsince the ultrathin sections are adhered directly to the surface of athick plastic tape (unlike lathe microtomes employing TEM imaging, wherethese ultrathin sections were supported only at their edges).

In addition to these improvements of the collection process, anautomatic lathe microtome configured for SEM imaging creates tissuetapes that can be more efficiently imaged. For example, the tissue tapescan be taken off the lathe microtome and immediately stained with heavymetals and SEM imaged, and no other processing may be required.

More specifically, in one exemplary example directed to SEM imaging, thetissue tape is cut into long strips (at points where there is notissue), and these strips are mounted onto the surface of a thin metalplate. The protective cover tape (which the automatic lathe microtomeadheres to the tissue tape during the collection process) is removed andthe plate with sections attached is bathed in heavy metal stainingsolutions. The resulting “tissue plate” is then mounted in an SEM havinga stage with large x-y range (like those designed for semiconductorwafer inspection whose stages can accept large wafers up to 300 mmwide). Any point on the plate's surface (i.e. any section of thecollected tissue) can thus be electron backscatter imaged within the SEMat resolutions in the nanometer range.

A set of a few dozen tissue plates would constitute an UltraThin SectionLibrary (UTSL), a permanent repository containing the ultrathin sectionsof a large volume of brain tissue. For example, with 50 nm sections aset of 100 plates would hold up to 50 cubic millimeters of tissue, anypoint of which could be imaged at nanometer resolution at any timesimply by loading the appropriate plate in the SEM. The automatic lathemicrotome can quickly create an UTSL of many cubic millimeters oftissue, enough to encompass multiple brain regions and theirinterconnecting axonal tracts. The UTSL can then be swiftly SEM imagedat intermediate resolution, and this can be used to intelligently directsubsequent (time intensive) high-resolution imaging forays. In this waya researcher can efficiently map out specific neural circuits spanningmany millimeters with a resolution in the nanometer range, a featimpossible with any other imaging technology.

More specifically, in one example, an ATLUM directed to SEM imagingproduces a continuous ribbon of thin tissue by lathing an extremely thinstrip off the surface of a cylindrical block containing one or amultitude of embedded tissue samples. This continuous ribbon of tissueis simultaneously collected onto a plastic support tape by the tapingmechanism of the ATLUM and is subsequently reeled up for later heavymetal staining and SEM backscatter imaging of the ultrathin tissuesections it contains.

An exemplary process according to one example starts by mounting thecylindrical tissue block on a metal axle that is held and rotated by ahigh-precision rotary stage. A diamond ultramicrotome knife (withattached water boat) is driven forward into the rotating block by meansof a high-precision linear stage capable of steps on the order of a fewnanometers. By synchronizing the rotational speed of the rotary stagewith the advancement speed of the knife, the knife's edge is caused totrace a spiral path through the cylindrical tissue block thus producinga continuous ribbon of tissue of the desired thickness. This process isexactly analogous to a conventional lathe producing a continuous “chip.”

The continuous ribbon of tissue produced in this manner comes streamingoff of the knife's edge and flows across the surface of the water in theknife's water boat. The automatic lathe microtome uses a conveyor belt(made of specially coated plastic tape) submerged in the water boat tocollect this streaming ribbon of tissue. The conveyor belt is drivensuch that its collection speed is closely matched to the knife's cuttingspeed. In this way, the ultrathin ribbon of tissue, which iscontinuously being produced at the knife's edge, floats for a short timeacross the water of the knife boat and is quickly collected by theconveyor belt of collection tape.

In the ATLUM, the fragile tissue ribbon is always under complete controlof the mechanism, being attached at one end to the block (from which itis being produced) and being attached at the other end to the collectiontape (submerged conveyor belt) to which it is being permanently attachedfor later imaging. The continuous nature of the ATLUM's sectioning andcollection process in this example, and its constant control of thefragile ribbon, allows the ATLUM to operate with complete autonomy andwith high reliability and to produce larger volumes of ultrathin tissuesections than any previous conventional microtome design.

In one aspect of this example, the ATLUM's tape collection mechanismincludes a continuous reel-to-reel mechanism containing a plastic film(tape) coated with carbon, as discussed in further detail below. Part ofthis tape web is submerged in the knife's water boat in order to collectthe tissue ribbon on the tape's carbon-coated surface. Immediately afterthe ribbon is collected on the collection tape an adhesive cover tape isapplied for protection during subsequent handling (this cover tape hasadhesive on its sides but not along its center, thus it protects thetissue ribbon without actually coming into contact with it). The final“tissue tape” (carbon-coated plastic film, collected tissue ribbon, andcover tape) is reeled up on a final take-up spool. Recall that allaspects of this collection process are continuous and are synchronizedwith the continuous cutting process.

The plastic film used in one example for preparation of a tissue tape isboPET, which is strong, does not wrinkle as it goes through themechanism, has an exceptionally smooth surface, and which has a highdegree of dimensional stability. The smooth surface is important forlater imaging since the tissue ribbon should lie down as flat aspossible on the tape. In some exemplary examples directed to SEMimaging, the boPET tape is coated with a layer of carbon (approximatelyone micron thick) on the side that will pick up the tissue. This carboncoating does three things: 1) it prevents charging in the SEM byproviding an electrically conductive path; 2) it prevents electron beamdamage by providing an efficient heat conductor under the tissue; and 3)it provides a highly uniform, low density (low z-number) substrate onwhich the tissue can rest. Since the tissue may be imaged via SEM usingbackscattered electrons it is important that the substrate itselfgenerate as little interfering backscatter signal as possible and carbonprovides this benefit. In other examples discussed in greater detailbelow, a polyimide tape such as Kapton® may be employed as a suitablesubstrate to facilitate SEM imaging.

Once collected, the tissue tape is cut into long strips (at points wherethere is no tissue), and these strips are mounted onto the surface of athin metal plate. The protective cover tape is removed and the platewith sections attached is bathed in heavy metal staining solutions. Thesolutions (typically uranyl acetate and lead citrate) stain selectedbiological structures within the sections with heavy (high z-number)atoms producing high electron backscatter signals during subsequent SEMimaging. The resulting “tissue plate” is then mounted in an SEM having astage with large x-y range and a researcher can subsequently use the SEMto image any point on the tissue plate at high resolution.

A single ATLUM run can potentially produce hundreds of meters of tissuetape from a single biological sample a few tens of cubic millimeters involume. This extremely long tape can then be used to produce a set ofapproximately 100 tissue plates. In this way the original biologicalsample has been reduced to an “UltraThin Section Library” (UTSL). Thisconcept of a UTSL is important to understanding the usefulness of theautomatic lathe microtome to researchers. For example, with 50 nm thicksections a set of 100 plates would hold up to 50 cubic millimeters oftissue, any point of which could be imaged at approximately 5 nm inplane resolution at any time simply by loading the appropriate plateinto the SEM. At this resolution this UTSL would potentially represent40,000 terabytes of imaging data. This is an almost unimaginable amountof data to store and process and the SEM imaging time required to imagethe entire UTSL is on the order of centuries. However, the UTSL itselfis quite compact (just one hundred plates) and any point within thismassive data set can be imaged at will by simply loading (e.g., manuallyor robotically) the corresponding tissue plate into an SEM.

The ability to efficiently direct nanometer resolution imaging anywherewithin a volume of many cubic millimeters of biological tissue is whatneuroscience researchers require to map the circuits of the brain. Atypical neural circuit includes several interconnected neurons eachsending long thin axonal processes many millimeters into separate brainregions. These axonal processes subsequently branch out and makesynaptic contacts within these regions that can only be seen withnanometer resolution imaging. Thus neuroscientists are faced with thesignificant challenge of producing nanometer resolution volume images oflarge volumes. The UTSL allows just that. The neuroscientist researchercan produce a UTSL containing the brain regions and connecting axonalpathways they wish to study. The researcher can then intelligentlydirect the SEM to image just those regions within the massive volumethat are needed to trace out the circuit of interest. Since the UTSL isa permanent repository of this neural volume, this or another researchercould easily follow-up on the original circuit study by tracingadditional branches of the very same neurons. In this way a single UTSLcould allow a whole set of collaborative circuits mapping studies over aseries of years, potentially revealing the complicated web of neuralcircuits the brain uses to perceive, remember, reason about, andpurposefully act upon the world.

Another example of the present invention is directed to closed-loopfeedback control in an ATLUM to regulate thickness of thin tissuesections or ribbons sliced from a block or bulk tissue sample. Asdescribed above, conventional microtomes typically move a tissue blockalong a linear path past a knife edge to produce a section, and thenretract the knife during a reset phase in preparation for the nextsection. For a lathe microtome, operation may be more continuous withoutneed for knife retraction. A tissue block may be mounted on an axlewhich may be rotated such that the tissue traces a circular path aroundthe rotational axis in close proximity to an advancing knife. As thetissue block moves along its circular path, it may intersect the knifeedge, allowing a section to be sliced off in the process. In variousexamples of the ATLUM design, sectioning performance may be improved,along with allowing thinner sectioning below 40 nm thick with greaterreliability and uniformity. The tissue sample to be sectioned may beembedded in and/or around a smooth axle and mounted on a rotary stage ofthe ATLUM. Capacitive sensors may be used to precisely measure thedistance between the knife edge and the axle surface. This distancemeasurement may be fed back to the knife stage via, but not limited to,an analog PID controller which endeavors to maintain a target distancefrom the knife edge to the axle surface. In this manner, variable forcesencountered at the knife edge during sectioning that would normallyproduce section thickness variations may be compensated in real time viaclosed-loop feedback control.

When attempting to cut very thin sections, it is advantageous to reducesection thickness variations where possible. For example, if a user wereattempting to section at 40 nm thickness and a variability of +/−20 nmexists in the knife edge position relative to the block, then one maycut 20 nm too thick on a part of the Nth section and 20 nm too thin onthe (N+1)th section. These two errors would combine to reduce a part ofthe (N+1)th section to zero thickness, leading to a break. Such breaks,if they occur often enough, may be problematic for automatic collectionof sections.

To address the foregoing, according to one example of the presentinvention one or more capacitive sensors mounted to the knife stage andpositioned so as to effectively measuring the distance from the knifeedge to the rotating steel axle containing the tissue block may allowfor the knife edge to be stabilized during sectioning to varysignificantly less than +/−20 nm. In some examples, knife edgestabilization may occur during sectioning such that section thicknessvariations are less than +/−10 nm. In further examples, knife edgestabilization may occur during sectioning such that section thicknessvariations are less than +/−5 nm. In even more examples, knife edgestabilization may occur during sectioning such that section thicknessvariations are less than +/−1 nm. Once section thickness variation issuitably limited, reliable sectioning may occur to thicknesses less than40 nm and lengths greater than 5 mm. From aspects presented herein,collection of hundreds of large area sections at thicknesses at or below50 nm may occur for large volume electron microscopic reconstructions ofbrain tissue.

Various aspects of an ATLUM configured with closed-loop feedback controlof sliced tissue thickness based on a capacitive sensing technique arediscussed in further detail below. For example, FIG. 6A shows a frontplan view of an ATLUM 1500 and FIG. 6B shows a perspective view of thesame ATLUM 1500 according to one example of the present invention inwhich closed-loop feedback control is implemented. In the figures, anair bearing rotary stage 700 may be securely mounted to an optical table702 floated on air for vibration isolation. A steel axle 704 with atissue sample may be mounted in the rotary stage 700 via a collet chuck.In some examples, the steel axle 704 may have a 0.5 inch diameter. Inother examples, the steel axle 704 may have a diameter greater than 1inch. A diamond knife stage 708 allows for the rotating block of tissuesample to be sectioned or sliced upon contact with a knife edge, and aconveyor belt collection mechanism 710 allows these sections to beautomatically collected on a substrate (or “support film”) supplied byfeed reel 712 to form a “tissue tape.” This tissue tape may betemporarily sealed with a protective top tape supplied by feed reel 714,and the assembly of substrate, sliced thin tissue, and protective toptape may be collected on the final take up reel 716. After completion ofa run, tape collected of ultrathin sections may be stained with heavymetals and imaged in a SEM using an electron backscatter signal, asdiscussed above, to produce high-quality, high-resolution images of thetissue's ultrastructure (e.g., sufficient for mapping the synapticconnectivity of brain tissue). It should be understood that in theexample shown, any suitable type of thin tissue section(s) or ribbon(s)may be produced. Tissue samples may be prepared for slicing in anyappropriate manner as well, such as through embedding, as describedpreviously. In various examples, a tissue sample may be mounted on arotatable axle 704 for slicing by placing a round block that containstissue to be sectioned around the axle 704. In further examples, atissue sample may be mounted on a rotatable axle 704 for slicing byplacing a block of any shape into a receiving portion of the axle 704which may be rotated such that the top of the block may be appropriatelysliced by the knife edge with each revolution of the rotatable axle 704.As discussed further below, the tissue samples mounted to the axle 704may be cylindrical in nature, or have wedge-like geometries.

In one example, the substrate supplied by feed reel 712 may exhibitqualities that enable the thin tissue sections mounted thereon to beimaged effectively using SEM techniques. In SEM, several high-voltageelectrons (˜10 kV) in an incident imaging beam typically pass throughthe thinly sliced tissue and interact with the substrate/support filmunderneath the tissue. If the support film degrades due to excessiveelectron exposure during imaging, the tissue above it will likelydegrade also. In this regard, one salient characteristic of a substratesuitable for use in SEM imaging of thinly sliced tissue includesresistance to bombardment with radiation and/or electrons. Anothersalient characteristic of a substrate suitable for use in SEM imaging oftissue sections includes a relatively high resistance to heat. In thisrespect, an exemplary suitable substrate has a high melting pointrelative to local temperatures found during SEM imaging and/or theability to conduct heat so that tissue is not exposed to hightemperatures for extended periods of time. Material containing atomswith low Z-number and atomic weight, providing little intrinsicbackscatter signal so as to not interfere with SEM and/or backscatteredelectron imaging, also provide a suitable substrate for SEM imaging ofthe thinly sliced tissue.

In some examples, as discussed above, the substrate upon which thintissue sections are mounted may be boPET (e.g., Mylar). In furtherexamples, so that the substrate exhibits a greater degree ofconductivity, substrates may incorporate a carbon additive in anysuitable form, such as, for example, in an extra layer deposited on thetop and/or bottom of the substrate. In other examples, the substrateupon which thin tissue sections are mounted may be polyimide (e.g.,Kapton® produced by DuPont™). Kapton® remains stable at temperatures upto 400 degrees Celsius and has excellent radiation resistance as well.In various examples, thin tissue sections may be collected directly onthe surface of bare Kapton® (without a previous carbon coat) andsubsequently a very thin layer (˜10 nm) of carbon may be deposited ontop of the tissue for charge dissipation purposes. In this respect, thistissue section thusly prepared may facilitate sufficient qualityhigh-resolution SEM images of the tissue while appearing to withstandmultiple, high-current image captures without damage to the tissue. Inaddition, use of bare or lightly carbon coated Kapton® makes the feedsubstrate materials for the ATLUM machine less expensive, avoidingdepositing a thick carbon coat (˜1 micron thick) onto the longcollection tape, which can be an expensive procedure. In general, usersof an ATLUM-created UTSL may often require that the same region of asection be imaged multiple times, for example when conducting multiscaleimaging or collecting a scanning electron tomographic tilt series. Inthis regard, collection of tissue on bare or lightly carbon coatedKapton® facilitates repetitive high resolution imaging.

FIG. 7 shows a closer view of the knife stage, tissue axle, and conveyorbelt collection mechanism. A wedge-shaped tissue sample 800 may bemounted on the rotatable axle 704, which may, as discussed above, bemounted in the rotary stage via a collet chuck 802. A diamondultramicrotome knife 804 may be attached to a piezo tilt stage 806 via amounting bracket 808. Mounting bracket 808 may also hold a pair ofcapacitive sensors 810 and 812. These capacitive sensors 810 and 812 maybe mounted at essentially the same height as the ultramicrotome knife804 edge, and configured to measure a distance between the knife edgeand the surface of the steel axle 704. Capacitive sensors 810 and 812may be mounted on either side of the knife, and thus their averageddistance measurement can effectively measure the distance of the knifeedge to the axle surface (with some absolute offset). This averaging ofsymmetrically mounted sensors can produce a distance measurement thatmay compensate for any wobble of the axle during its rotation. It shouldbe understood that any appropriate type and number of sensors may beused to measure the distance between knife edge and the steel axle 704.Indeed, it is possible for only one sensor to be used in measuring thisdistance. The sensor may function in any suitable manner, one examplebeing through a capacitive sensing system. As a result, from knowing therate at which the knife edge moves towards the steel axle 704 and therotational velocity of the tissue block around the steel axle 704, thethickness of the resulting sliced tissue section may be suitablyestimated. Floating tissue section 814 may be collected from a waterboat positioned along with the knife 804 via a partially submergedconveyor belt 816 or any other appropriate method.

FIG. 8A shows the piezo tilt stage 806 from a side plan view withsensors 810 and 812 removed in this view for clarity. A fulcrum 900 ofthe tilt stage 806 may be positioned directly below the edge of theknife 804. In this respect, the largest cutting forces may be absorbedby the stiffest part of tilt stage 806. When a linear piezo actuatorwithin tilt stage 806 expands it causes the knife to rotate forwardaround fulcrum point 900. This tilt causes the knife edge 902 to moveforward toward axle 704 and to cut off a section of tissue wedge 800 asthe axle 704 rotates.

As mentioned above, in one aspect, the tilt stage 806 compensates forvariable forces encountered during sectioning. The greatest force on theknife 804 during sectioning is often the force that occurs in thedirection that the knife is plowing through the tissue, which force isdepicted in FIG. 8A by force vector 905. In various examples, thefulcrum point 900 may be placed directly in line with this forcecomponent, reducing torque that may arise which also could move theknife. Smaller forces applied to the knife edge in the directiondepicted by force vector 904 may occur during sectioning as well, givingrise to a likelihood for the knife to move away from the axle due to thestage's finite tilt stiffness and due to the stage's finite x-stiffness(x direction parallel to arrow 904). In one aspect, the tilt stage 806may be piezo actuated, allowing for ˜5 nm positioning resolution of theknife edge. In this regard, due to construction of the piezo tilt stage,tilt stiffness and x-stiffness may both be coupled to the piezo actuatorand may thus be compensated. When using capacitive feedback (e.g., viathe capactive sensors 810 and 812), an integral control term mayeffectively provide infinite stiffness, limited by bandwidth, to thepiezo actuator. As the tilt stage may couple forces at the knife edge tothe piezo actuator, the knife edge may be effectively rigid relative tothe axle 704 surface, allowing for reductions in section thicknessvariations such that large block faces may be sectioned at thicknessesat or below 50 nm. It should be understood that any suitable actuationmechanism may be incorporated in operation of the tilt stage, including,but not limited to, piezo actuation, electromechanical actuation, or anyother appropriate method.

It is noted that as a result of use of a tilt stage, as the knifeadvances during a run, the clearance angle of the knife may change. Insome instances, changing clearance angle may be problematic if theclearance angle were to change drastically; however, in the exampledepicted in FIGS. 7 and 8, the clearance angle may change by only afraction of a degree over the full range of knife travel, which may beapproximately ˜300 microns.

FIG. 8B shows the piezo tilt stage 806 from a side plan view withcapacitive sensor 810 also shown. The distance that the sensors 810 and812 are measuring is depicted by dimension 906. This distance may betightly controlled by a controller 908 which drives the piezo actuatorin tilt stage 806. In some examples, the controller 908 may be aproportional-integral-derivative controller or any other suitablefeedback controlling device.

FIG. 5A shows another close-up side view of the piezo tilt stage 806shown in FIGS. 7 and 8, further illustrating the conveyor belt 816partially submerged in the water of a water boat 950 behind the edge 902of knife 804. The water boat may be incorporated directly behind theknife edge such that the surface tension of the water may support thefragile thin tissue section as it is being sliced from the tissue sample800 on the rotatable axle 704. The surface tension may provide asuitable frictionless support for the thin tissue section, allowing itto stream smoothly off the knife edge. The submerged conveyor belt 816may also be provided in the water boat close to the knife edge runningat a similar speed to that of the tissue sections streaming off theknife edge. In this manner, each tissue section may be gently collectedonto the surface of the conveyor belt. The curved bottom 1000 of thewater boat 950 is depicted with a dashed line to show how conveyor belt816 dips into the water but does not scrape the bottom 1000 of the waterboat. In this respect, the angle that the edge of the water boat makeswith a tangent of the steel axle 704 at the point of slicing may berelatively coincident so that a thin tissue section may come off theaxle 704 smoothly and into the water boat. In one example of operation,FIG. 9B shows a tissue block with a protruding tissue wedge 800 mountedon to the steel axle 704 that rotates in proximity to the knife 804. Inthis example, once the tissue wedge 800 rotates into the knife edge, athin tissue section may be smoothly sliced off on to the water surfaceof the water boat. The thin tissue section may then migrate towards theconveyor belt 816 which takes up the thin tissue section for furtherprocessing.

In another aspect of the present invention, lathe microtomes may sectioncylindrical blocks of tissue sample, wedge shaped blocks (which arepartial cylinders that do not extend all the way around the rotaryaxle), or any other shape that may be suitably sectioned. Whensectioning a cylindrical block of tissue sample, the knife smoothlyadvances while the block is rotated. The knife does not disengage fromthe block of tissue sample and traces a spiral path through thecylindrical block, producing a continuous ribbon of thinly slicedtissue. This process is similar to how a rotary lathe cuts continuouswood veneers by rotating a log past a very wide knife edge. Whensectioning a wedge shaped block of tissue sample for a desired sectionthickness, the knife may be stepped forward once per revolution duringthe part of the rotation cycle when the tissue wedge is not being cut bythe knife. The knife may then be left in place or may move only slightlyforward during the part of the rotation cycle when the knife issectioning the wedge. In these block sectioning modes, rotational motionof the lathe is not required to reverse direction, and knife motion isnot required to retract, typically moving forward into the block. Inthis respect, such attributes, including having stable cuttingperformance, make lathe microtomes appropriate for automated sectioncollection techniques.

In different examples presented herein, if a continuous ribbon 820 oftissue is being sectioned from a full cylindrical block of tissuesample, as shown in FIG. 10A, then the ribbon 820 may extend from theknife edge, across the water boat for a few millimeters, and to theconveyor belt, where the ribbon 820 may be continuously collected. Inthis regard, the conveyor belt collection speed should be well matchedto the sectioning speed.

In other examples, if a partial cylinder block, or wedge of tissuesample, is being sectioned then it should be considered whether the thinsliced tissue section has a relatively longer length 822, i.e., longerthan the distance from the knife edge to the conveyor belt, as shown inFIG. 10B, or whether the sliced tissue section has a relatively shortersection length 824, i.e., shorter than the distance from the knife edgeto the conveyor belt, as shown in FIG. 10C. In both of these cases eachsection may be momentarily secured only at the knife edge while theleading edge of the section is pushed toward the conveyor belt by themomentum of the rest of the section being created behind it. For sectionlengths 822 that are longer than the distance from the knife edge to theconveyor belt, in order to minimize the tendency for the thin tissuesection to bend on its way to the conveyor belt, it may be beneficialfor the knife edge to be accurately adjusted so that it is relativelyparallel to the tangent of the rotational axis of the lathe at the pointof contact. To further minimize tendencies for the thin tissue sectionto bend on its way to the conveyor belt, the section width may berelatively wide compared to the distance from the knife edge to theconveyor belt. As an example, for a 7 mm distance from the knife edge tothe conveyor belt, a section width of 1-2 mm may be used. Further, forreliable collection and full automation to be achieved, the conveyorbelt collection speed should be well matched to the sectioning speed.

If the section length 824 is shorter than the distance from the knifeedge to the conveyor belt, as shown in FIG. 10C, the sections can stillbe collected reliably and automatically, where the Nth section maysimply be pushed toward the conveyor belt by the (N+1)th section. Inthis respect, the leading and trailing edges of each section should berelatively straight to prevent the free Nth section from being pushed atan angle by the (N+1)th section. This condition may be met by being surethat the wedge shaped block of tissue sample is shaped such that theleading and trailing edges are substantially parallel to the knife edge.Also, for a greater degree of collection reliability and ability forfull automation to be achieved, the knife edge may be accuratelyadjusted so that it is relatively parallel to the tangent of therotational axis of the lathe at the point of contact. In addition, thesection width may be relatively wide compared to the distance from theknife edge to the conveyor belt. For the case where the section lengthis shorter than the distance from the knife edge to the conveyor belt,it should be noted that it is not necessary for the conveyor beltcollection speed to be well matched to the sectioning speed, but theconveyor belt collection speed should be fast enough to ensure thatsections do not bunch up in the water boat.

III. MOVABLE AUTOMATED COLLECTION APPARATUSES, SYSTEMS AND METHODS

In various inventive embodiments described herein, a collectionapparatus may be constructed to be mobile with respect to the microtome,with the ability to be positioned in and out of coupled engagement withany microtome, as appropriately desired. FIGS. 11A-11C illustrate anembodiment of a system 2000 for producing thin tissue sections byslicing a tissue sample, and collecting the thin tissue sections on to asupport substrate. The system 2000 includes a collection apparatus 2100coupled with a microtome 2200 and with certain aspects of the systemcontrolled by a computing device 2300. In the embodiment illustrated,the microtome 2200 is a conventional microtome that functions to slice atissue sample into thin tissue sections which may float on a liquidsurface once they are cut from the microtome knife. The collectionapparatus 2100 is positioned at an orientation so as to be engaged withthe microtome 2200 to automatically and suitably collect the thin tissuesections from fluid contained within a reservoir 2210 of the microtome.As discussed above, the collection apparatus may be coupled to anysuitable microtome known in the art. Collection apparatuses discussedare particularly suitable to be coupled with microtomes where thintissue sections, upon slicing, come into contact with a fluid surface.In some embodiments, the sole region of physical contact between thecollection apparatus 2100 and the microtome 2200 is through the fluiddisposed within the reservoir 2210 of the microtome.

A tissue sample is secured in an appropriate position on the microtomefrom which thin tissue sections are sliced, as can be appreciated bythose having ordinary skill in the art. When sliced, for certainembodiments, a thin tissue section slides away from the knife of themicrotome on to a surface of fluid (e.g., water) having a surfacetension that permits the thin tissue sections to float across the fluidsurface. The thin tissue sections are then collected on to a supportsubstrate (e.g., a support tape) where the support substrate moves up aconveyor portion 2110 of the collection apparatus toward a take-upregion.

In some embodiments, and without limitation, the collection apparatus2100 may be suitably attached to a first base portion 2150 which iscoupled to a second base portion 2151, as shown in FIG. 12. Either orboth of the base portions 2150, 2151 may be weighted so as to keep thecollection apparatus in a firm position. Although firmly secured when inoperation, for some embodiments, the collection apparatus 2100 is notpermanently coupled to the microtome. A rack and pinion 2158, 2160 isattached to first base portion 2150 for moving the collection apparatus2100 in a vertical motion illustrated in FIG. 12 by double sided dashedarrow v. Second base portion 2151 is coupled to a slide rail 2152 havinga lock 2154 that is suitable for fixing the collection apparatus 2100 inplace, when desired. Accordingly, collection apparatus 2100 may move ina horizontal motion depicted by double sided dashed arrow h. Verticaland horizontal movement of the collection apparatus relative to themicrotome will be described in more detail below.

As shown in FIGS. 13A and 13B, the collection apparatus 2100 can beremoved from engagement with the microtome 2200 such that the collectionapparatus is not in a suitable position for automatic collection of thintissue sections from the microtome. FIG. 13A depicts, for example,raising of the collection apparatus 2100 in a direction d₃ so that theconveyor portion 2110 of the collection apparatus comes out of contactwith the fluid contained within the reservoir 2210. In some embodimentsas discussed above, and without limitation, the collection apparatus canbe moved vertically through engagement with a rack and pinion post 2160(e.g., 2 inch wide post) having a knob 2158 for adjusting the height ofthe collection apparatus relative to the microtome. Once a suitableheight for the collection apparatus is reached, for example, when theconveyor portion 2110 has sufficient clearance from the top of a wall ofthe reservoir 2210, the rack and pinion post 2160 may be suitably locked(e.g., via a clamp) in place from further vertical motion.

The collection apparatus 2100 may also be constructed to move along aslide rail 2152 upon which the collection apparatus 2100 may slidetoward or away from the microtome when not in a coupled arrangement withthe microtome for collecting tissue sections. For example, as shown inFIG. 13B, after the collection apparatus 2100 is raised from a positionwhere the conveyor portion 2110 had been operatively oriented in amanner suitable to automatically collect tissue sections from themicrotome 2200, the collection apparatus may slide horizontally alongthe rail 2152 in a direction opposite d₁ (along the dashed arrow) to aposition further away from the microtome. At any point along the sliderail 2152, lock 2154 can be used to secure the collection apparatus in astationary position. Upon positioning of the collection apparatus in anon-collecting position a sufficient distance away from the microtome, auser is permitted to perform activities related to routine usage of themicrotome, such as block trimming or knife setup, for example. When thecollection apparatus is positioned away from the microtome, a user maymanually collect tissue sections, for example, using the conventionaleyelash collection method.

The collection apparatus 2100 may be moved from a non-collectingposition in a positive direction d₁ and into a collecting position wherethe apparatus is in a coupled arrangement with the microtome; that is,where automated retrieval of thin tissue sections may suitably occurfrom the microtome on to portions of the collection apparatus. Forexample, the collection apparatus may move along rail 2152 toward themicrotome and, when in a suitable horizontal position with respect tothe reservoir 2210, may be lowered in a direction opposite d₃ into anappropriate position for automated collection of tissue sections.

A positioning feature 2156 may facilitate placement of the collectionapparatus in a suitable collecting position. In some embodiments, apositioning feature 2156 includes a pedestal for preventing thecollection apparatus from being excessively lowered. For some cases, itmay be detrimental for the conveyor portion 2110 of the collectionapparatus 2100 to be lowered beyond the surface of the fluid containedwithin the reservoir 2210 in a manner, for example, where the conveyorportion forcibly contacts the bottom of the reservoir. A positioningfeature 2156 may incorporate a pedestal to serve as a stop feature uponlowering the collection apparatus so that a user is not required to makeprecise readjustments each time the collection apparatus is to be placedin a collecting position. For some cases, positioning feature 2156 mayinclude a pin adjustment for the collection apparatus to be suitablyplaced at a desired height. For example, in a pin adjustment, a pin maybe placed along various points in a support structure corresponding todifferent heights for the collection apparatus to be positioned.Accordingly, if a user determines that a collection apparatus should beplaced at a collecting position that is lower than a previous collectingposition, a pin may be pulled out of an existing socket and placed intoa socket corresponding to a lower position.

Placing the collection apparatus into a collecting position involves anarrangement that suitably results in automatic and continuous retrievalof thin tissue sections on to a support substrate for long periods oftime. As discussed above, a collection apparatus initially located at anon-collecting position a distance away from the microtome may be movedtoward the microtome and placed into a coupled arrangement with themicrotome, as shown in FIGS. 14A and 14B. For example, part of theconveyor portion (e.g., a tip) of the collection apparatus may bepartially submerged into a fluid contained within a reservoir of themicrotome.

In some embodiments, coupling of the collection apparatus with themicrotome involves horizontally positioning the collection apparatus ina direction along with or opposite d₁ so that the conveyor portion iscentered with respect to the fluid reservoir. For example, the distancebetween side edges of the conveyor portion and side walls of thereservoir may be about 0.5 mm. Once the collection apparatus ishorizontally centered, the vertical position of the collection apparatusmay then be adjusted to ensure that the support substrate will besubmerged in the fluid, without scraping against the bottom of thereservoir. Further, the collection apparatus may be adjusted in aforward-backward direction along or opposite d₂ so as to set anappropriate distance between the edge of the microtome knife and thepoint of collection; that is, the point where the support substrateemerges from the fluid. In some embodiments, the distance between theedge of the microtome knife and the point of collection is slightlylonger than the length of a sliced tissue section. FIG. 14A depicts asuitable position of the conveyor portion 2110 of the collectionapparatus with respect to the reservoir 2210 of the microtome. As shownin FIG. 14B, the reservoir 2210 contains an appropriate fluid 2212having a surface tension suitable for supporting thin tissue sectionssliced from the knife of the microtome.

In some embodiments, rather than straight horizontal and/or verticalmovement of the collection apparatus with respect to the microtome, asystem may provide for the collection apparatus to be rotated towardand/or away from coupled arrangement with the microtome. For example,the collection apparatus could be arranged to rotate about a pivot (notshown in the figures) with respect to the microtome.

Although movement of the collection apparatus 2100 relative to themicrotome 2200 has been described with respect to manual operation, itshould be appreciated that such movement of the collection apparatusinto and out of a collecting position may occur automatically. Forexample, an operator that observes a collection apparatus positionedaway from the microtome in a non-collecting position may easily initiatean automated collection process by sending a command (e.g., pressing abutton) to a control system having actuators that automatically move thecollection apparatus into a suitably coupled arrangement with themicrotome.

Turning back to the embodiment shown in FIG. 12, a vertical actuator3010 is coupled to the collection apparatus 2100 for automatically andsuitably moving the collection apparatus 2100 in a vertical motion inaccordance with double sided dashed arrow v. In addition, horizontalactuator 3020 is coupled to the first base portion 2150 of thecollection apparatus for automatically and suitably moving thecollection apparatus 2100 in a horizontal motion along double sideddashed arrow h via slide rail 2152. As such, vertical actuator 3010 andhorizontal actuator 3012 may be in communication with a suitablecomputer-controlled device so as to function in tandem to mechanicallymove the collection apparatus into and out of a collecting position.Actuators 3010, 3012 may include appropriate electrical and/ormechanical components (e.g., solenoids, actuators, motors, etc.) thatenable suitable movement of the collection apparatus without requirementfor a user to manually move the collection apparatus between collectingand non-collecting positions. Any suitable number of actuators coupledbetween a controller and the collection apparatus may be used. Forexample, additional actuators for fine, coarse, linear and/or rotationalmovement of the collection apparatus may be incorporated. The system mayalso employ feedback to determine whether the collection apparatus is ina collecting position. For example, the position of the collectionapparatus may be tracked through a video monitoring device and, throughfeedback to the controller, a signal may be sent to the actuator(s) toadjust the position (e.g., vertically, horizontally, rotationally, etc.)of the collection apparatus accordingly.

In some cases, the system may also be configured to automaticallycommence production and collection of thin tissue sections on to asupport substrate when the collection apparatus is in an appropriateposition. Thus, by initiating a simple command, actuators coupled to thecollection apparatus may move the collection apparatus into suitableengagement with the microtome and once in the collecting position,automated collection of thin tissue sections is initiated. Once thintissue sections are sufficiently collected, the system may furtherprovide for automatic movement of the collection apparatus away from themicrotome. Thus, for some cases, collection of thin tissue sections maybe completely automated.

As tissue sections are collected, fluid is typically lost due toevaporation from the reservoir and removal of fluid by the supportsubstrate. In some embodiments, fluid in the reservoir of the microtomeis automatically maintained at a constant level during operation of thecollection apparatus, compensating for fluid loss and ensuring thatfluid is continually available at the edge of the microtome knife.Maintaining contact of tissue sections with fluid provides forappropriate lubrication of the tissue sections as well as surfacetension support of the tissue sections on the fluid once cut from theknife. In manual collection schemes, fluid levels are not automaticallymaintained, and fluid may be added, as appropriately desired. However,when tissue sections are automatically collected, despite continual lossof fluid, it is advantageous for fluid levels to be kept constantwithout need for user intervention. It should be appreciated that anysuitable fluid may be provided in the reservoir. For example, the fluidmay be water, an aqueous solution or a non-aqueous solution.

In a representative embodiment, a reservoir contains water maintained ata level where the edge of the microtome knife is continuously wet duringsample cutting. That is, the level of water is at least close enough tothe knife to form a concave meniscus or is at a level that is even withthe edge of the knife, keeping the cutting edge of the knife wet. Insome cases, the water level is kept at a level slightly lower than theknife edge so that the concave meniscus wets the edge of the knife,enabling the tissue sections to slide down a slope formed by the concavemeniscus.

A system including a computing device may be coupled to a videomonitoring device for assessing the current level of fluid in areservoir and a fluid input apparatus (e.g., perfusion pump, syringe,etc.) for introducing fluid into the reservoir when desired. Thecomputing device may be used to send signals as a controller in afeedback system for automatically maintaining the level of fluid in thereservoir. The computing device records and analyzes video images of thefluid level in the reservoir by detecting the dark-to-light boundary ofa reflective sheen produced by the fluid.

In an example, a computing device 2300 may provide a user interface2310, as illustratively shown in FIG. 15A. In some embodiments, a flatwater surface 2214 may reflect white diffuse light into a videomonitoring device and is recorded as a uniform white color in the videoimage. A concave meniscus formed with the edge of the knife 2230, on theother hand, may produce an angle of reflection from the water such thatrecorded video images of the meniscus are black in color. The contrastin image between a flat water surface reflection 2214 and a concavemeniscus may be apparent as a boundary 2216 recorded from the imagingapparatus. A contrast sensing region 2320, depicted in FIG. 15A as aslender rectangle, may be traced out in the recorded image to quantifywhere the boundary 2216 is located, defining the distance between theknife edge 2230 and the edge of the concave meniscus. Such a method ofmeasure provides a sensitive technique in measuring the current level ofwater in the reservoir so as to provide an indication of whether a knifeedge maintains wetness in a manner where thin tissue sections may becollected automatically over prolonged periods of time.

The computing device performs image analysis of the video informationgathered from the video monitoring device and determines the distanceof, for example, the concave meniscus from the edge 2230 of the knife.When the surface of water extends a distance from the knife edge that isbeyond a threshold for suitable operation of tissue section collection,a small amount of water is injected into an appropriate region of thereservoir so as not to interfere with collection (e.g., with minimalturbulence). For example, and without limitation, the dark region of thevideo, signifying the presence of the concave meniscus, is maintainedfor suitable operation of the automatic collection system such that anedge of the dark region closest to the edge of the knife extends betweenabout 0.2 mm and about 0.5 mm from edge of the knife, as measured by thecontrast sensing region 2320. When the computing device detects, fromthe video information, that the edge of the dark region extends beyond0.5 mm from the edge of the knife (e.g., due to evaporation, transportby movement the support substrate, etc.), an appropriate signal is sentto the input apparatus for an increment of water (e.g., about 0.05 mL orless, or about 0.02 mL or less) to be introduced into the reservoir.Conversely, for some embodiments, when the computing device detects thatthe fluid level is too high, or for example, extends above the knifeedge 2230, fluid may be appropriately removed from the reservoir. Itshould be appreciated that the threshold boundaries for which the systemis alerted to introduce into or remove fluid from the reservoir may varyas appropriately desired. Although not so limited, the distance betweenthe knife edge 2230 and an edge of a tip 2116 of the conveyor portionmay be about 5 mm, as shown in FIG. 15A.

In some embodiments, so that the water level does not increase tooquickly to cause tissue sections to undesirably drift away from suitablelocations for support substrate retrieval, the computing device may sendappropriate signal(s) to the input apparatus to pause for a brief periodof time (e.g., at least about 30 seconds) between subsequent injections.In some embodiments, the total fluid volume introduced into thereservoir of a microtome at a particular interval, when the currentfluid level is detected to be less than a threshold of an operatinglevel, is between about 0.05 mL and about 0.20 mL, for example, about0.10 mL.

Control interface 2310 may include control features, such as thosedepicted in FIG. 15A. A time stamp 2330 may be provided, for example,indicating to a user what the time is during a collection process run orfor how long a collection process has been run. The interface may alsoinclude a intensity profile 2340 measured across the contrast sensingregion 2320 as a time averaged pixel intensity of the recorded image. Insome embodiments, the location of the boundary 2216 between the flatwater surface and the concave meniscus is determined by assessing thepixel position along the contrast sensing region 2320 where the changein intensity is greatest. The location of the boundary 2216 across thecontrast sensing region 2320 may be indicated by a position indicator2342. The threshold for determining at what position the boundary 2216is to be located to trigger input of additional fluid may be set by auser through the interface 2310 via a threshold control 2344. Anindicator 2346 may also be provided to alert a user when the thresholdof the boundary 2216 exceeded.

With respect to other aspects of water filling provided by the userinterface 2310, the minimum time between each discrete input of watermay be set using control 2350. For example, if it is desired for thefluid input apparatus to pause for more than 30 seconds beforeintroducing additional fluid into the reservoir, the time lapse betweenfilling can be set to a greater time increment. An indicator 2352 mayalso show to the user the time since a last fluid input has occurred.User interface 2310 may include an alarm 2360 to alert the user whenfluid levels are low. As such, the threshold for signaling the alarm maybe set according to the threshold control 2344, or may be set accordingto another suitable level of measure.

The user interface 2310 may also permit a user to activate anddeactivate certain features of the controller. For example, an alarmsilence switch 2370 may be provided for a user to silence alarmsassociated with the system, as desired. In some cases, silencing ofalarms may not be advisable since, when an alarm is silenced, a user maybe less prone to be aware of a situation that requires adjustment (e.g.,when the fluid level in the reservoir is too low and tissue sections arenot being collected properly on to the support substrate). In addition,fluid input switch 2380 may also be provided, which permits thecontroller to send a signal to the fluid input apparatus for automaticfluid input into the reservoir without user intervention. Deactivatingthe fluid input switch 2380 may turn off the automatic fluid inputfeature, requiring a user to manually input fluid into the reservoir asneeded.

An embodiments of a fluid input apparatus setup 2400 shown in FIGS. 15Band 15C includes an automatic input device 2410 and a manual inputdevice 2420. The automatic input device 2410 includes a pump 2412, apump controller 2414 and a channel 2416. Pump 2412 and channel 2416 arein fluid communication with the reservoir of the microtome. The pumpcontroller 2414 may be connected with a controller of the computingdevice 2300 and may receive signals for the automatic input device 2410to introduce fluid from pump 2412 into the reservoir through the channel2416. The pump controller 2414 includes an actuating portion thatapplies an appropriate force to the pump 2412 when an actuation signalis received from the computing device 2300. Alternatively, a user maymanually input fluid into the reservoir from manual input device 2420,shown in FIG. 15B as a syringe, through channel 2422 which are also influid communication with the reservoir. FIG. 15C shows a close up viewof an input nozzle 2430 having a spout leading to the reservoir and influid communication with channel 2416 of the automatic input device2410. Input nozzle 2440 is also shown to have a spout for fluid inputinto the reservoir and in fluid communication with channel 2422 of themanual input device 2420. Input nozzles may be arranged so thatturbulence is minimized upon fluid input into the reservoir.

Controlling the level of fluid within the reservoir of the microtome mayenable automated collection of tissue sections for extended periods oftime. In some embodiments, absent a method for the fluid level in areservoir to be maintained, automated collection runs may last untilfluid levels are in need of replenishment (e.g., about 30 minutes);though, by implementing a manner under which fluid levels may be tightlycontrolled, collection runs may last for several days at a time.

In certain representative embodiments, thin tissue sections may becollected on to a moving support tape that is stored on a take up reelprior to imaging. As illustrated in FIGS. 16A-16C, though not meant tobe limiting, the collection apparatus 2100 may include a support tapefeed reel 2120 mounted on a support tape feed reel holder 2121, a covertape feed reel 2122 mounted on a cover tape feed reel holder 2123, and atake up reel 2124 mounted on a take up reel holder 2125.

The support tape feed reel 2120 provides a support tape 2102 forcollecting thin tissue sections on to a top surface of the support tape.In this regard, the support tape feed reel 2120 rotates in a clockwisedirection from the perspective of a viewer of FIG. 16A, as depicted bythe dashed arrow. The cover tape feed reel 2122 rotates in acounter-clockwise direction, along the corresponding dashed arrow, inproviding a cover tape 2104 that may be optionally applied to thesupport tape having thin tissue sections disposed thereon. Although notrequired, when a cover tape 2104 is applied on to the thin tissuesections disposed on the underlying support tape, the cover tape may beappropriately aligned with the support tape via an applicator 2180 oncethe support tape comes off the back end of the conveyor portion 2110.Further, the take up reel 2124 rotates in a counter-clockwise direction,depicted by the dashed arrow on take up reel 2124, to collect the finalsupport substrate 2106 having thin tissue sections disposed, at least,on a support tape.

While not expressly shown, any of the reels may be appropriately removedand/or replaced when desired. For example, when the support tape feedreel 2120 is empty or when take up reel 2124 is at full capacity, eitheror both of these reels may be replaced by a user, or alternatively, by asuitable automated reel replacement system. Reels on a collectionapparatus may be easily and conveniently replaceable. For example, reelholders may be firm to hold respective reels in place during operation,yet deformable so that reels can be conveniently removed and replaced.Reel holders may be suitably manufactured, for example, to includerubber prongs, or to have a suitable insert mechanism (e.g., slotinsert) that allows a reel to be conveniently mounted and removed fromthe holder. In some cases, reels may be mounted on a reel holder via asuitable interference fit.

In some embodiments, portions of reels described may be transparent,allowing a user to clearly observe how much tape (e.g., support tape,cover tape, recovered tape on a take up reel) remains on a particularreel. For example, if there is very little support tape remaining on asupport tape feed reel 2120, then a user may remove the feed reel andreplace it with a reel having more feed stock of support tape. If thetake up reel 2124 is at full capacity or almost at full capacity, theuser may remove the take up reel, for further processing/imaging of thetissue sections on the take up reel at a later time, and replace it withan empty take up reel. A full feed reel may be sufficiently long (e.g.,over 40 m long) for several collection runs to be performed. Forexample, if a support substrate is about 50 microns in thickness,approximately 10,000 thin tissue sections can be collected, spaced about4 mm apart.

For some embodiments, it may not be desired for tissue sections to besandwiched between a cover tape and a support tape; that is, for a covertape to be applied to a support tape. Hence, collection runs can beperformed without including a cover tape feed reel 2122 mounted on thecover tape feed reel holder 2123. Though, when desired, a cover tapefeed reel 2122 may be conveniently and suitably be placed on cover tapefeed reel holder 2123, and used as desired. In one embodiment, where acover tape is not used, the top roller of the top pinch drive isoriented such that the roller only presses down on the sides of thesupport tape. For example, for an 8 mm wide support tape, the top pinchdrive may touch only 2 mm strips on each side of the support tapeleaving the middle 4 mm of the support tape untouched. Accordingly, thepinch drive roller does not interfere with or crush the tissue sectionsthat are collected along the middle of the support tape.

While FIGS. 16A and 16B depict a collection apparatus 2100 absent one ormore base portions and the microtome, FIG. 16C provides an illustrationof collection apparatus 2100 disposed in a suitable coupling positionwith respect to the microtome. In operation, a support tape 2102 may bedriven by bottom pinch drive 2130 to move from the support tape feedreel 2120 along rollers of the bottom pinch drive 2130, through aportion of a tension monitoring device 2140 and toward conveyor portion2110. The support tape 2102 moves along a bottom surface of the conveyorportion 2110 and into a surface of fluid contained within the reservoir2210. As the support tape 2102 moves around the tip of the conveyorportion and out of the fluid, the support tape 2102 collects thin tissuesections sliced from the microtome floating on the surface of the fluid.The support tape 2102 having thin tissue sections disposed thereonsubsequently moves along a surface of the conveyor portion and towardapplicator 2180 which applies cover tape 2104 to an upper surface of thesupport tape 2102. The support substrate combination 2106, having thintissue sections disposed between support tape 2102 and cover tape 2104,then moves through top pinch drive 2132 and is collected into take upreel 2124. In some embodiments, when sectioning of a tissue sample bythe microtome occurs, the above tissue section collecting process isautomatically initiated on the collection apparatus.

In some embodiments, the support tape feed reel holder 2121, cover tapefeed reel holder 2123 and take up reel holder 2125 incorporate a builtin a slip clutch that engages with respective reels to maintain tapetension during operation of the collection apparatus. For example, aslip clutch may be built in to a reel holder so that a user is notrequired to adjust friction settings for proper engagement of a supportor cover tape upon changing a corresponding reel. A slip clutch may alsoprovide automatic compensation in tension for when the speed or geometryof the support substrate changes. In one embodiment, reel holders 2121,2123, 2125 are, at appropriate times, driven in a reverse direction(e.g., with an electric motor) at a constant rate. Driving reel holdersin a reverse direction, in combination with built-in slip clutches, mayassist to ensure that the tape has a constant tension as the tape entersin and exits from the pinch drives. Such motion may avoid the occurrenceof stick-slip of static friction.

As discussed above, the collection apparatus 2100 may optionally includea dual pinch drive configuration. In this respect, a bottom pinch drive2130 may be disposed at a position upstream from take up of tissuesections before the support tape engages with the conveyor portion 2110and the reservoir 2210. A top pinch drive 2132 may be disposed at adownstream position where tissue sections have already been collected onto the support tape. Pinch drives may be used to advance the supporttape along the collection apparatus at a speed and tension suitable forautomated collection of thin tissue sections for extended periods oftime.

In some embodiments, the collection apparatus 2100 includes a tensionmonitoring device 2140 which provides feedback to a controller (e.g.,computing device) regarding tension in the support tape. The controller,in turn, makes a determination as to whether settings in the top and/orbottom pinch drive should be adjusted to increase or decrease tension inthe support tape. In an embodiment, tension monitoring device 2140 mayinclude a spring-loaded dangler arm attached to a potentiometer toprovide information about the tension in the support tape. Based on adesired tension for the support tape (e.g., to be maintained at aconstant tension), actuation of pinch drives 2130, 2132 may be adjustedaccordingly. For example, once presented with data from thepotentiometer regarding the spring length of the dangler arm (i.e., thetension of the support tape), the controller makes a determination as towhether the spring length is within suitable operating conditions. Ifthe spring length is outside of suitable operating conditions, the topor bottom pinch drive, or both, are adjusted to increase or decrease thesupport tape tension so as to maintain the spring length to be withinoperating conditions. In some cases, the tension of a support tape willbe tightly controlled so as to minimize interference with the collectionprocess, for example, arising from disturbances in the fluid of thereservoir.

In some embodiments, a feedback control mechanism is used to suitablymaintain the rate of movement of the support tape on the collectionapparatus. The speed of a support tape may be appropriately monitored,such as for example, by an optical encoder device (not expressly shown)that sends an electrical signal to the controller of the collectionapparatus. Based on the speed of the support tape, the controller maysend out a signal that results in actuation of components (e.g., a DCgear motor) of the top and/or bottom pinch drive. In some cases, thespeed of a support tape is controlled to match the sectioning speed ofthe microtome, allowing for the collection process to be smooth andcontinuous.

The speed and tension of a support tape moving along a collectionapparatus may be subject to a feedback mechanism (e.g., closed loop oropen loop) controlled by a computing device using a suitable program(e.g., LabVIEW) that collects information regarding the speed andtension of the support tape through appropriate measuring techniques. Insome embodiments, the speed and tension of the support tape duringcollection may be maintained at a user-specified range. For example, thespeed and tension of the support tape may be kept by the controllersystem to be substantially constant. As discussed above, for someembodiments, pinch drives in feedback with the controller areappropriately actuated to maintain speed and/or tension of the supporttape within suitable parameters. In some embodiments, reel holders areactuatable to drive a support tape along the collection apparatus,according to desired ranges of speed and/or tension.

A conveyor portion 2110 of a collection apparatus 2100 may be suitablyconstructed to facilitate automated collection of thin tissue sectionson to a support substrate (e.g., support tape). FIG. 17 shows anembodiment of a conveyor portion 2110 that includes a collection surface2112 upon which a support substrate may move along having collected anumber of thin tissue sections. In some embodiments, the collectionsurface 2112 may be structured to have an inclination for guiding thesupport tape up from the fluid surface of the reservoir and into asubsequent portion of the collection apparatus for subsequent take up(e.g., application of cover tape and collection by a take up reel). Insome cases, as shown in FIG. 17, collection surface 2112 additionallyprovides a relatively horizontal surface for the support tape to movealong. The collection surface 2112 may provide a low-friction surface(e.g., Teflon, nylon) upon which a support tape may readily slide. Thecollection surface 2112 may have any suitable width, for example,between about 8 mm and about 10 mm wide, such as about 8.2 mm wide.

Side walls 2114 may act as barriers to the collection surface 2112guiding the support substrate to maintain movement in a substantiallystraight direction along the conveyor. Side walls 2114 may include anysuitable material, such as, and without limitation, stainless steel.

Conveyor tip 2116 may have a small radius of curvature, enabling thepoint of collection of thin tissue sections to be in close proximity tothe edge of the knife. While for some instances, a conveyor tip 2116 mayinclude a roller device, for other instances, a conveyor tip 2116includes a rigid surface that is non-rotatable so as to minimize thecollection of dirt on the conveyor and/or the occurrence of turbulencein the fluid through extraneous movement.

The position of conveyor portion 2110 may be finely adjusted in anyappropriate direction by any suitable manner. In some embodiments, auser may provide a fine adjustment of the height and/or the distance ofthe conveyor tip from the edge of the microtome knife and relative tothe reservoir. Such fine adjustment may have a range, for example, overa distance of up to about 10 mm. An example shown in FIGS. 18 and 19includes adjustment knobs 2170 that are conveniently accessible by auser for manipulating the position of conveyor portion 2110 with respectto the collection apparatus. As such, conveyor portion 2110 may beadjusted so that the conveyor tip 2116 is appropriately positioned withrespect to the fluid in the reservoir 2210 and locked in place. In somecases, a height adjust knob 2172 may be used to manipulate the height ofthe conveyor portion 2110; an angle adjust knob 2174 may be suitable forchanging the angle of orientation of the conveyor tip 2116 with respectto the fluid; and a forward-backward adjust knob 2176 may be employedfor adjusting the distance of the conveyor portion 2110 relative to themicrotome knife. When appropriate fine positional adjustments are made,the conveyor portion may be suitably locked in place, for example, witha tightening mechanism 2178 (e.g., wing nut), as shown in FIG. 19.

It should be appreciated for those of skill in the art that fineadjustments of the conveyor portion 2110 with respect to the collectionapparatus 2100 may be automatic in nature. That is, a control system candetermine what fine adjustments of the conveyor portion should be madefor suitable positioning relative to the microtome knife. Accordingly,electrical signals may be sent to one or more actuators of thecollection apparatus to provide for appropriate movement of the conveyorportion. Alternatively, a user can finely adjust the position of theconveyor portion relative to the collection apparatus without having toturn knobs, but by operating a control system that is suitably coupledwith the collection apparatus.

In embodiments discussed, a collection apparatus may operate for over 12hours; or days at a time. Accordingly, it may not be desirable for anoperator to be required to observe the collection process over longperiods of time. In some embodiments, video information of thecollecting process may be suitably recorded to evaluate at what pointthere may have been lost or damaged tissue sections while the operatorwas away from the system. For example, a suitable video monitoringdevice may be used to verify correct operation of thin tissue sectionsas they come off of the knife edge and are collected. In an embodiment,the user interface of the fluid level control program described aboveincludes a positionable box in the video images that records thelight/dark contrast of each tissue section as it comes off the knife forcollection. Video monitoring will make a record if a tissue sectionhappens not to be sliced. Also, if a thin tissue section is too thin orthick, then the color of the section as recorded on the video image(s)will change, and be noted by the system. Monitoring collection of thintissue sections by assessing the color of the sections is described inU.S. Patent Publication No. 2010/0093022 entitled “Methods andApparatuses for Providing and Processing Sliced Thin Tissue.”

The system 2000 may be appropriately shielded from environmentaldisturbances, such as for example, air drafts or abrupt changes intemperature. In some embodiments, the system 2000 may be surrounded byan environmental enclosure 2500, such as that shown in FIG. 20, so thatundesirable environmental occurrences do not detrimentally interferewith operation of the collection process. The environmental enclosure2500 may, without limitation, be suitable a plexiglass case, or otherappropriate device.

IV. CONCLUSION

Having thus described various illustrative embodiments, it is to beappreciated that various alterations, modifications, and improvementswill readily occur to those skilled in the art. Such alterations,modifications, and improvements are intended to be part of thisinvention, and are intended to be within the spirit and scope of thisinvention. While some examples presented herein involve specificcombinations of functions or structural elements, it should beunderstood that those functions and elements may be combined in otherways according to the present invention to accomplish the same ordifferent objectives. In particular, acts, elements, and featuresdiscussed in connection with one embodiment are not intended to beexcluded from similar or other roles in other embodiments. Accordingly,the foregoing description and attached drawings are by way of exampleonly, and are not intended to be limiting.

Any suitable embodiments described as well as implied herein can beimplemented in any of numerous ways. For example, the embodiments may beimplemented using hardware, software or a combination thereof. Whenimplemented in software, the software code can be executed on anysuitable processor or collection of processors, whether provided in asingle computer or distributed among multiple computers.

Further, it should be appreciated that a computing device may beembodied in any of a number of forms, such as a rack-mounted computer, adesktop computer, a laptop computer, or a tablet computer. Additionally,a computing device may be embedded in a device not generally regarded asa computer but with suitable processing capabilities, including aPersonal Digital Assistant (PDA), a smart phone or any other suitableportable or fixed electronic device.

Also, the computing device may have one or more input and outputdevices. These devices can be used, among other things, to present auser interface. Examples of output devices that can be used to provide auser interface include printers or display screens for visualpresentation of output and speakers or other sound generating devicesfor audible presentation of output. Examples of input devices that canbe used for a user interface include keyboards, and pointing devices,such as mice, touch pads, and digitizing tablets. As another example, acomputing device may receive input information through speechrecognition or in other audible format.

Also, the various methods or processes outlined herein may be coded assoftware that is executable on one or more processors that employ anyone of a variety of operating systems or platforms. Additionally, suchsoftware may be written using any of a number of suitable programminglanguages and/or conventional programming or scripting tools, and alsomay be compiled as executable machine language code or intermediate codethat is executed on a framework or virtual machine.

In this respect, embodiments may include a computer readable medium (ormultiple computer readable media) (e.g., a computer memory, one or morefloppy discs, compact discs, optical discs, magnetic tapes, flashmemories, circuit configurations in Field Programmable Gate Arrays orother semiconductor devices, or other non-transitory medium or tangiblecomputer storage medium, etc.) encoded with one or more programs that,when executed on one or more computing devices, computers, or otherprocessors, perform methods that implement the various embodiments ofthe invention discussed above. The computer readable medium or media canbe transportable, such that the program or programs stored thereon canbe loaded onto one or more different computers or other processors toimplement various aspects of the present invention as discussed above.

The terms “program” or “software” are used herein in a generic sense torefer to any type of computer code or set of computer-executableinstructions that can be employed to program a computing device,computer or other processor to implement various aspects of the presentinvention as discussed above. Additionally, it should be appreciatedthat according to one aspect of this embodiment, one or more computerprograms that when executed perform methods of the present inventionneed not reside on a single computing device, computer or processor, butmay be distributed in a modular fashion amongst a number of differentcomputing devices, computers or processors to implement various aspectsof the present invention.

Computer-executable instructions may be in many forms, such as programmodules, executed by one or more computers or other devices. Generally,program modules include routines, programs, objects, components, datastructures, etc. that perform particular tasks or implement particularabstract data types. Typically the functionality of the program modulesmay be combined or distributed as desired in various embodiments.

Also, data structures may be stored in computer-readable media in anysuitable form. For simplicity of illustration, data structures may beshown to have fields that are related through location in the datastructure. Such relationships may likewise be achieved by assigningstorage for the fields with locations in a computer-readable medium thatconveys relationship between the fields. However, any suitable mechanismmay be used to establish a relationship between information in fields ofa data structure, including through the use of pointers, tags or othermechanisms that establish relationship between data elements.

Various aspects of the present invention may be used alone, incombination, or in a variety of arrangements not specifically discussedin the embodiments described in the foregoing and is therefore notlimited in its application to the details and arrangement of componentsset forth in the foregoing description or illustrated in the drawings.For example, aspects described in one embodiment may be combined in anymanner with aspects described in other embodiments.

Also, the invention may be embodied as a method, of which an example hasbeen provided. The acts performed as part of the method may be orderedin any suitable way. Accordingly, embodiments may be constructed inwhich acts are performed in an order different than illustrated, whichmay include performing some acts simultaneously, even though shown assequential acts in illustrative embodiments.

The invention claimed is:
 1. A non-transitory computer-readable storagemedium comprising computer-executable instructions that, when executedby at least one processor, perform a method of processing a tissuesample, the method comprising: monitoring, by the at least oneprocessor, a production rate of thin tissue sections produced by slicingof the tissue sample with a microtome-quality knife; and controlling, bythe at least one processor, motion of a support substrate moving on acollection apparatus in accordance with the production rate of the thintissue sections to collect the plurality of thin tissue sections on thesupport substrate.
 2. The non-transitory computer-readable storagemedium of claim 1, wherein monitoring the production rate of thin tissuesections produced by slicing of the tissue sample comprises recordingvideo information.
 3. The non-transitory computer-readable storagemedium of claim 1, wherein the method further comprises monitoring atension of the support substrate moving on the collection apparatus. 4.The non-transitory computer-readable storage medium of claim 3, whereinmonitoring the tension of the support substrate comprises recordinginformation from a potentiometer.
 5. The non-transitorycomputer-readable storage medium of claim 3, wherein the method furthercomprises controlling the tension of the support substrate moving on thecollection apparatus based on the monitoring of the tension of thesupport substrate.
 6. The non-transitory computer-readable storagemedium of claim 5, wherein controlling the tension of the supportsubstrate comprises maintaining the tension of the support substrate tobe substantially constant.
 7. The non-transitory computer-readablestorage medium of claim 5, wherein controlling the tension of thesupport substrate comprises controlling at least one tensioning deviceto adjust the tension of the support substrate.
 8. The non-transitorycomputer-readable storage medium of claim 1, wherein the method furthercomprises monitoring a speed of the support substrate moving on thecollection apparatus.
 9. The non-transitory computer-readable storagemedium of claim 8, wherein monitoring the speed of the support substratecomprises recording information from an optical encoder device.
 10. Thenon-transitory computer-readable storage medium of claim 1, whereincontrolling the motion of the support substrate comprises maintaining aspeed of the support substrate to be substantially constant.
 11. Thenon-transitory computer-readable storage medium of claim 1, whereincontrolling the motion of the support substrate comprises controlling atleast one drive device to adjust a speed of the support substrate movingon the collection apparatus.
 12. The non-transitory computer-readablestorage medium of claim 1, wherein controlling the motion of the supportsubstrate comprises controlling a speed of the support substrate.
 13. Amethod of processing a tissue sample, the method comprising: monitoring,by at least one processor, a production rate of thin tissue sectionsproduced by slicing of the tissue sample with a microtome-quality knife;and controlling, by the at least one processor, motion of a supportsubstrate moving on a collection apparatus in accordance with theproduction rate of the thin tissue sections to collect the plurality ofthin tissue sections on the support substrate.
 14. The method of claim13, wherein monitoring the production rate of thin tissue sectionsproduced by slicing of the tissue sample comprises recording videoinformation.
 15. The method of claim 13, further comprising monitoring atension of the support substrate moving on the collection apparatus. 16.The method of claim 13, further comprising monitoring a speed of thesupport substrate moving on the collection apparatus.
 17. The method ofclaim 16, wherein monitoring the tension of the support substratecomprises recording information from a potentiometer.
 18. The method ofclaim 13, wherein controlling the motion of the support substratecomprises controlling a speed of the support substrate.